HATCHERY AND GENETIC MANAGEMENT PLAN

Hatchery Program: Clearwater Spring and Summer Chinook Salmon (Clearwater Fish Hatchery)

Spring/summer Chinook Salmon Species or Oncorhynchus tshawytscha. Hatchery Stock: South Fork, Powell, and Clear Creek stocks

Agency/Operator: Idaho Department of Fish and Game

Watershed and Region: Clearwater River, Idaho.

Date Submitted:

Date Last Updated: November 2011

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EXECUTIVE SUMMARY

The management goal for the Clearwater Spring Chinook salmon population is to provide sustainable fishing opportunity and to enhance the natural spawning population. While the Snake River Spring- and Summer-Run Chinook Salmon Ecological Significant Unit (ESU) was listed as threatened under the Endangered Species Act (ESA) on August 22, 1992, the non-indigenous hatchery spring-run Chinook stocks currently found in the Clearwater River and its tributaries are not listed under the ESA because the historical populations in the basin were likely extirpated following construction of Lewiston Dam in 1927.

The purpose of the Clearwater River spring Chinook hatchery program is to mitigate for fish losses caused by the construction and operation of the four lower Snake River federal dams. The hatchery mitigation program is a federally authorized mandate to annually return 12,000 adult spring Chinook salmon to stream reaches upstream of Lower Granite Dam after harvest of 48,000 adults by commercial and sport fisheries in the ocean, the Columbia River and the lower Snake River. Current hatchery production and supplementation efforts from this program are consistent with the 2008-2017 US vs. Oregon Management Agreement. Fish culture is performed at the Clearwater Hatchery. Broodstock collection occurs at the Red River, Crooked River, and the Powell satellite facilities and at Kooskia Hatchery (Clear Creek). Hatchery operations and monitoring activities are funded by the Bonneville Power Administration through the Lower Snake River Compensation Plan (LSRCP). Where appropriate, other sources of funding for monitoring activities are identified.

Juvenile releases from the segregated programs will occur in the Lochsa River (400,000 spring- run smolts); Selway River (400,000 spring-run smolts and 300,000 spring-run parr); Red River (SF Clearwater) (1.1 million spring-run smolts); Clear Creek (235,000 spring-run smolts); and Crooked River (200,000 summer-run smolts). Locally adapted broodstock will be used for the Lochsa River, South Fork Clearwater and Clear Creek programs. Broodstock from one of these sites will be used for releases in the Selway River program until such time as infrastructure is in place to collect broodstock in the Selway River.

This mitigation program has never achieved the escapement goal of 12,000 adults to the project area since the inception of the program. Based on the most recent 10 year geometric mean SAR of 0.34% to Lower Granite dam (Red River, Crooked River and Powell combined), the production capacity at this facility needs to be increased to 3.5 million yearling smolts to return 12,000 adults to the project area under recent Columbia River harvest schedules.

Early in the program, managers agreed (through the USvOR process) to scale back the steelhead production goals that were originally modeled for the program to meet the mitigation goal of returning 14,000 steelhead back to Lower Granite Dam. This reduction in steelhead production provided additional rearing space for Chinook salmon at Clearwater Fish Hatchery. Managers have prioritized the use of that space to increase the production of spring- and summer-run Chinook salmon at Clearwater Fish Hatchery.

The original production target for spring Chinook salmon was 1.4 million yearling smolts. Currently, 2,135,000 spring-run Chinook yearling smolts are reared at Clearwater Fish Hatchery.

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Of the total release, 135,000 smolts are not adipose fin clipped and do not contribute to mark selective fisheries. Additionally, 500,000 subyearling spring Chinook salmon, primarily intended for supplementation, are reared at Clearwater Fish Hatchery.

In addition to the existing spring Chinook program, managers have initiated the development of a locally adapted summer-run Chinook salmon population in the Clearwater River. Anecdotal accounts of wild Chinook returns to Clearwater basin prior to their extirpation suggest that they may have included both spring- and summer-run populations. IDFG, the Nez Perce Tribe, and the LSRCP initiated a program in 2009 to evaluate the potential of building a locally adapted hatchery population and supplement naturally spawning summer-run Chinook salmon populations in the Clearwater River drainage. Eggs from the harvest portion of the McCall Hatchery program on the South Fork Salmon River are being incubated and reared at the Clearwater Fish Hatchery. The smolts will be released in the Crooked River in the upper South Fork Clearwater drainage. Adult returns from those releases will be trapped at the Clearwater Hatchery Crooked River trapping facility and used to develop a locally adapted and fully independent summer-run broodstock for subsequent harvest and supplementation releases in the Selway and South Fork Clearwater rivers. Egg transfers from the McCall Hatchery will cease once a locally adapted broodstock is developed in the Clearwater River.

Key performance standards for the program will be tracked in a targeted monitoring and evaluation program. These standards include: (1) abundance and composition of natural spawners and hatchery broodstock (pHOS, pNOB, and PNI); (2) number of smolts released; (3) in-hatchery and post-release survival rates; (4) total age specific adult recruitment, harvest and escapement of the natural and hatchery components; and (5) abundance, productivity, diversity and spatial structure of the naturally spawning Chinook populations.

SECTION 1. GENERAL PROGRAM DESCRIPTION

1.1 NAME OF HATCHERY OR PROGRAM

Hatchery: Clearwater Fish Hatchery

Program: Clearwater Spring Chinook

1.2 SPECIES AND POPULATION (OR STOCK) UNDER PROPAGATION, AND ESA STATUS

The species being propagated is Spring Chinook salmon (Oncorhynchus tshawytscha).

The Snake River Spring- and Summer-Run Chinook Salmon ESU was listed as threatened under the Endangered Species Act (ESA) on August 22, 1992 and reaffirmed on June 28, 2005. The ESU includes those fish that spawn in the Snake River drainage and its major tributaries, including the Grande Ronde River and the Salmon River, and that complete their adult, upstream migration (passing Bonneville Dam) between March and July. The non-indigenous hatchery spring- and summer-run Chinook stocks currently used in the Clearwater River and its tributaries are not considered part of the ESU (57 FR 14653). Native spring Chinook salmon were likely

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extirpated from the Clearwater River subbasin following the construction of Lewiston Dam in 1927.

Source: HSRG 2009

Figure 1. Clearwater River Spring Chinook MPG.

1.3 RESPONSIBLE ORGANIZATION AND INDIVIDUALS

Lead Contact

Name (and title): Pete Hassemer, Anadromous Fish Manager. Agency or Tribe: Idaho Department of Fish and Game. Address: 600 S. Walnut, P.O. Box 25, Boise, ID 83707. Telephone: (208) 334-3791. Fax: (208) 334-2114. Email: [email protected]

On-site Operations Lead Page 4

Name (and title): Jerry McGehee, Fish Hatchery Manager II. Agency or Tribe: Idaho Department of Fish and Game. Address: 4156 Ahsahka Rd., Ahsahka, ID 83520. Telephone: (208) 476-3331. Fax: (208) 479-3548. Email: [email protected]

Other agencies, Tribes, co-operators, or organizations involved, including contractors, and extent of involvement in the program:

IDFG, the Nez Perce Tribe, the Lower Snake River Compensation Plan office and the U.S. Fish and Wildlife Service collaboratively develop and implement production plans to meet mitigation goals and productions goals outlined in the U.S. vs. OR 2008-2017 Management Plan. The same agencies meet collaboratively to co-author Annual Operating Plans for the Clearwater River Spring/Summer Chinook Salmon programs at Clearwater Hatchery and they work collaboratively in –season to meet shared broodstock needs for the Clearwater Hatchery Dworshak Hatchery, Kooskia Hatchery, and Nez Perce Tribal Hatchery programs. IDFG coordinates with the Nez Perce and Oregon Department of Fish and Wildlife and Washington Department of Fish and Wildlife to manage state and tribal fisheries for harvest shares and ESA take. Harvest and hatchery management coordination includes pre-season planning, scheduled weekly meetings and post-season summary meetings to share information and identify management actions required to meet tribal and state fishery objectives.

Specific responsibilities of other agencies are as follows:

U.S. Fish and Wildlife Service – Lower Snake River Compensation Plan Office: Administers the Lower Snake River Compensation Plan as authorized by the Water Resources Development Act of 1976.

Nez Perce Tribe: The Clearwater Fish Hatchery incubates eggs and rears juvenile Chinook salmon for the Nez Perce Tribal supplementation program as identified in the 2008-2017 Management Agreement associated with the development of the Columbia River Fish Management Plan under the U.S. v Oregon process.

1.4 FUNDING SOURCE, STAFFING LEVEL, AND ANNUAL HATCHERY PROGRAM OPERATIONAL COSTS

The U.S. Fish and Wildlife Service funds this program under the Lower Snake River Compensation Plan. Annual budget: $1,887,000.

Staffing level: 8 permanent staff and 152 months of temporary staff time. This budget accounts for both steelhead and Spring/summer Chinook salmon production.

1.5 LOCATION(S) OF HATCHERY AND ASSOCIATED FACILITIES

Clearwater Fish Hatchery - The program consists of the main hatchery and three satellite facilities. The Clearwater Fish Hatchery is located at confluence of the North Fork and mainstem Clearwater rivers, river kilometer 65 on the Clearwater River; 121 Page 5

kilometers upstream from Lower Granite Dam, and 842 kilometers upstream from the mouth of the Columbia River. The Hydrologic Unit Code is 17060300800100.00.

Red River - The Red River satellite facility is located at river kilometer 27 of the Red River, a tributary to the South Fork of the Clearwater River at river kilometer 101. The facility is 310 kilometers upstream from Lower Granite Dam and 1,030 kilometers from the mouth of the Columbia River. The Red River pond was built in 1977 under the Columbia River Fisheries Development Project and was administered by NMFS, IDFG, USFS, and the Pacific Northwest Regional Commission until 1986. In 1986, a permanent adult trapping facility and holding complex was constructed by the U.S. Army Corps of Engineers as part of the LSRCP.

Crooked River - The Crooked River satellite facility is located at river kilometer 1 of Crooked River, also a tributary to the South Fork Clearwater River at river kilometer 94. The facility is 287 kilometers upstream from Lower Granite Dam and 1,007 kilometers upstream from the mouth of the Columbia River. The Crooked River satellite has been in operation since 1990.

Powell - The Powell satellite facility is located at the headwaters of the Lochsa River (river kilometer 0), at the confluence of Brushy Fork Creek and Colt Killed Creek (previously White Sand Creek). The Lochsa River is a tributary to the Middle Fork Clearwater. The satellite facility is 320 kilometers upstream from Lower Granite Dam and 1,040 kilometers upstream from the mouth of the Columbia River.

1.6 TYPE OF PROGRAM

This hatchery program is operated as a segregated harvest program. A component of the program (approximately 17% of the current production) is intended to provide a supplementation benefit consistent with the 2008-2017 US vs. OR Management Agreement. Clearwater hatchery also conducts early rearing for spring Chinook salmon (200,000) that are transferred to the Nez Perce Tribal Fish Hatchery (NPTH) and subsequently reared to full-term smolts and released from the NPTH into the mainstem Clearwater River.

1.7 PURPOSE (GOAL) OF THE PROGRAM

The management goals for the Clearwater River spring Chinook populations are to provide sustainable fishing opportunities and to increase the abundance of the natural populations. These populations are not listed under the Endangered Species Act because the wild populations in the basin were likely extirpated following construction of Lewiston Dam in 1927.

The purpose of the Clearwater River spring Chinook hatchery program is to mitigate for fish losses caused by the construction and operation of the four lower Snake River federal dams. The hatchery mitigation program is a federally authorized mandate to annually return 12,000 adult spring Chinook salmon to stream reaches upstream of Lower Granite Dam after a harvest of 48,000 in downstream fisheries. Hatchery production for harvest mitigation and supplementation efforts from this program are also mandated in US vs. Oregon. Fish culture is performed at the Clearwater Hatchery, Red River Satellite Facility, Crooked River Satellite Facility, and the Powell Satellite Facility. All hatchery operations and monitoring activities are

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funded by the Bonneville Power Administration through the Lower Snake River Compensation Plan.

The Clearwater River spring/summer Chinook hatchery program is part of the Lower Snake River Compensation Plan (LSRCP), a congressionally mandated program pursuant to PL 99-662. The purpose of the LSRCP is to replace adult salmon, steelhead and rainbow trout lost by construction and operation of four hydroelectric dams on the Lower Snake River. Specifically, the stated purpose of the plan is:

“…[to]….. provide the number of salmon and steelhead trout needed in the Snake River system to help maintain commercial and sport fisheries for anadromous species on a sustaining basis in the Columbia River system and Pacific Ocean” (NMFS & USFWS 1972 pg 14)

Specific mitigation goals for the LSRCP were established in a three step process. First, the adult escapement that occurred prior to construction of the four dams was estimated. Second, an estimate was made of the reduction in adult escapement (loss) caused by construction and operation of the dams (e.g. direct mortality of smolt). Third, a catch to escapement ratio was used to estimate the future production that was forgone in commercial and recreational fisheries as result of the reduced spawning escapement and habitat loss. Assuming that the fisheries below the project area would continue to be prosecuted into the future as they had in the past, LSRCP adult return goals were expressed in terms of the adult escapement back to, or above the project area. Other than recognizing that the escapements back to the project area would be used for hatchery broodstock, no other specific priorities or goals were established in the enabling legislation or supporting documents regarding how these fish might be used. For spring Chinook salmon the escapement above Lower Granite Dam prior to construction of these dams was estimated at 122,200 adults. Based on a 15% mortality rate for smolts transiting each of the four dams (48% total mortality) the expected reduction in adults subsequently returning to the area above Lower Granite Dam was 58,700. This number established the LSRCP escapement mitigation goal. This reduction in natural spawning escapement was estimated to result in a reduction in the coast-wide commercial/tribal harvest of 176,100 adults, and a reduction in the recreational fishery harvest of 58,700 adults below the project area. In summary the expected total number of adults that would be produced as part of the LSRCP mitigation program was 293,500.

Component Number of Adults Escapement above Lower Granite Dam 58,700 Commercial Harvest 176,100 Recreational Harvest 58,700 Total 293,500

Since 1976 when the LSRCP was authorized, many of the parameters and assumptions used to size the hatchery program and estimate the magnitude and flow of benefits have changed. The survival rate required to deliver a 4:1 catch to escapement ratio has been less than expected and this has resulted in fewer adults being produced. The listing of Spring Chinook under the Endangered Species Act has resulted in significant curtailment of commercial, recreational and tribal fisheries throughout the

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mainstem Columbia River. This has resulted in a higher percentage of the annual run returning to the project area than was expected. The U.S. v. Oregon court stipulated Fishery Management Plan has established specific hatchery production agreements between the states, tribes and federal government. This agreement has substantially diversified the spring Chinook hatchery program by adding new off-station releases sites and stocks designed to meet short term conservation objectives. The Clearwater River spring Chinook salmon mitigation program was designed to escape 12,000 adults back to the project area after a harvest of 48,000. While recognizing the overarching purpose and goals established for the LSRCP, and realities’ regarding changes since the program was authorized, the following objectives for the beneficial uses of adult returns have been established for the period through 2017:

1. To contribute to the recreational, commercial and/or tribal fisheries in the mainstem Columbia River consistent with agreed to abundance based harvest rate schedules established in the 2008 – 2017 U.S. vs. Oregon Management Agreement. 2. To collect approximately 1900 spring-run and 120 summer-run adult broodstock to perpetuate this hatchery program (see sections 6-8 for more detail). 3. To provide recreational and tribal tributary fisheries annually (see Section 3.3 for more detail). 4. To utilize hatchery-origin adults for supplementing the natural population.

To maximize the beneficial uses of fish that return to the project area that are not used for broodstock, harvest or natural spawning, managers have developed agreements to share and distribute these fish equally between tribal and non-tribal entities. Specific objectives are established annually as part of a preseason co-manager meeting between the states, tribes and federal agencies to prioritize the distribution of fish, Specific dispositions may include: a. Tribal subsistence b. Recycling fish back through terminal fisheries c. Donations to food banks and charitable organizations d. Outplanting for natural spawning e. Nutrient enhancement

1.8 JUSTIFICATION OF PROGRAM

The Clearwater River spring/summer Chinook hatchery program is part of the Lower Snake River Compensation Plan (LSRCP), a congressionally mandated program pursuant to PL 99-662. The purpose of the LSRCP is to replace adult salmon, steelhead and rainbow trout lost by construction and operation of four hydroelectric dams on the Lower Snake River.

Segregated harvest type programs will be operated in the Lochsa River (400,000 smolts), Selway River (400,000 smolts, 300,000 parr), South Fork Clearwater River (1.1 million smolts) and Clear Creek (235,000 smolts). Locally adapted broodstock will be used for the Lochsa River, South Fork Clearwater and Clear Creek programs. Non-locally adapted broodstock will be used for the Selway River program until such time as infrastructure is in place to collect broodstock

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locally. A component of the Clearwater Fish Hatchery production capacity is utilized to provide a supplementation benefit in the Selway River. This production is identified in the 2008-2017 USvOR Management Agreement.

1.9 LIST OF PROGRAM PERFORMANCE STANDARDS

“Performance Standards” are designed to achieve the program goal/purpose, and are generally measurable, realistic, and time specific. The NPPC “Artificial Production Review” document attached with the instructions for completing the HGMP presents a list of draft “Performance Standards” as examples of standards that could be applied for a hatchery program. If an ESU-wide hatchery plan including your hatchery program is available, use the performance standard list already compiled.

Upon review of the NPCC “Artificial Production Review” document (2001) we have determined that this document represents the common knowledge up to 2001 and that the utilization of more recent reviews on the standardized methods for evaluation of hatcheries and supplementation at a basin wide ESU scale was warranted.

A NPCC “Artificial Production Review” document (2001) provides categories of standards for evaluating the effectiveness of hatchery programs and the risks they pose to associated natural populations. The categories are as follows: 1) legal mandates, 2) harvest, 3) conservation of wild/naturally produced spawning populations, 4) life history characteristics, 5) genetic characteristics, 6) quality of research activities, 7) artificial production facilities operations, and 8) socio-economic effectiveness. The NPCC standards represent the common knowledge up to 2001.

In a report prepared for Northwest Power and Conservation Council, the Independent Scientific Review Panel (ISRP) and the Independent Scientific Advisory Board (ISAB) reviewed the nature of the demographic, genetic and ecological risks that could be associated with supplementation, and concluded that the current information available was insufficient to provide an adequate assessment of the magnitude of these effects under alternative management scenarios (ISRP and ISAB 2005). The ISRP and ISAB recommended that an interagency working group be formed to produce a design(s) for an evaluation of hatchery supplementation applicable at a basin-wide scale. Following on this recommendation, the Ad Hoc Supplementation Workgroup (AHSWG) was created and produced a guiding document (Galbreath et al. 2008) that describes framework for integrated hatchery research, monitoring, and evaluation to be evaluated at a basin-wide ESU scale.

The AHSWG framework is structured around three categories of research monitoring and evaluation: 1) implementation and compliance monitoring, 2) hatchery effectiveness monitoring, and 3) uncertainty research. The hatchery effectiveness category addresses regional questions relative to both harvest augmentation and supplementation hatchery programs and defines a set of management objectives for specific to supplementation projects. The framework utilizes a common set of standardized performance measures as established by the Collaborative Systemwide Monitoring and Evaluation Project (CSMEP). Adoption of this suite of performance measures and definitions across multiple study designs will facilitate coordinated analysis of findings from regional Page 9

monitoring and evaluation efforts aimed at addressing management questions and critical uncertainties associated with relationships between harvest augmentation and supplementation hatchery production and ESA listed stock status/recovery.

The NPCC (2006) has called for integration of individual hatchery evaluations into a regional plan. While the RM&E framework in AHSWG document represents our current knowledge relative to monitoring hatchery programs to assess effects that they have on population and ESU productivity, it represents only a portion of the activities needed for how hatcheries are operated throughout the region. A union of the NPCC (2001) hatchery monitoring and evaluation standards and the AHSWG framework likely represents a larger scale more comprehensive set of assessment standards, legal mandates, production and harvest management processes, hatchery operations, and socio-economic standards addressed in the 2001 NPCC document (sections 3.1, 3.2, 3.7, and 3.8 respectively). These are not addressed in the AHSWG framework and should be included in this document. NPCC standards for conservation of wild/natural populations, life history characteristics, genetic characteristics and research activities (sections 3.3, 3.4, 3.5, and 3.6 respectively) are more thoroughly in the AHSWG and the later standards should apply to this document. Table 1 represents the union of performance standards described by the Northwest Power and Conservation Council (NPCC 2001), regional questions for monitoring and evaluation for harvest and supplementation programs, and performance standards and testable assumptions as described by the Ad Hoc Supplementation Work Group (Galbreath et al. 2008).

Table 1. Compilation of performance standards described by the Northwest Power and Conservation Council (NPCC 2001), regional questions for monitoring and evaluation for harvest and supplementation programs, and performance standards and testable assumptions as described by the Ad Hoc Supplementation Work Group (Galbreath et al. 2008).

Category Standards Indicators

1.1.1. Total number of fish harvested in Tribal fisheries targeting this 1.1. Program contributes to fulfilling tribal program. trust responsibility mandates and 1.1.2. Total fisher days or proportion of harvestable returns taken in treaty rights, as described in Tribal resident fisheries, by fishery. applicable agreements such as under 1.1.3. Tribal acknowledgement regarding fulfillment of tribal treaty U.S. v. OR and U.S. v. Washington. rights. 1.2. Program contributes to mitigation 1.2.1. Number of fish released by program, returning, or caught, as

requirements. applicable to given mitigation requirements. LEGAL LEGAL MANDATES 1.3. Program addresses ESA 1.3.1. Section 7, Section 10, 4d rule and annual consultation

responsibilities. 1. 2.1.1. Hatchery is operated as a segregated program. 2.1. Program contributes to mitigation 2.1.2. Hatchery is operated as an integrated program requirements. 2.1.3. Hatchery is operated as a conservation program 2.2.1. Hatchery fish can be distinguished from natural fish in the 2.2. Program addresses ESA hatchery broodstock and among spawners in supplemented or responsibilities. hatchery influenced population(s) 2.3.1. Hatchery and natural-origin adult returns can be adequately forecasted to guide harvest opportunities. 2.3. Restore and maintain treaty-reserved

2.3.2. Hatchery adult returns are produced at a level of abundance COMPLIANCE IMPLEMENTATIONAND tribal and non-treaty fisheries. adequate to support fisheries in most years with an acceptably

limited impact to natural-spawner escapement. 2.

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Category Standards Indicators

2.4. Fish for harvest are produced and 2.4.1. Number of fish release by location estimated and in compliance released in a manner enabling with AOPs and US vs. OR Management Agreement. effective harvest, as described in all 2.4.2. Number if adult returns by release group harvested applicable fisheries management 2.4.3. Number of non-target species encountered in fisheries for plans, while avoiding over-harvest of targeted release group. non-target species. 2.5.1. Juvenile rearing densities and growth rates are monitored and reported. 2.5. Hatchery incubation, rearing, and 2.5.2. Numbers of fish per release group are known and reported. release practices are consistent with 2.5.3. Average size, weight and condition of fish per release group are current best management practices known and reported. for the program type. 2.5.4. Date, acclimation period, and release location of each release group are known and reported. 2.6.1. Production adheres to plans documents developed by regional co-managers (e.g. US vs. OR Management agreement, AOPs etc.). 2.6. Hatchery production, harvest 2.6.2. Harvest management harvest, harvest sharing agreements, management, and monitoring and broodstock collection schedules, and disposition of fish trapped evaluation of hatchery production are at hatcheries in excess of broodstock needs are coordinated coordinated among affected co- among co-management agencies. managers. 2.6.3. Co-managers react adaptively by consensus to monitoring and evaluation results. 2.6.4. Monitoring and evaluation results are reported to co-managers and regionally in a timely fashion. 3.1. Release groups are marked in a 3.1.1. All hatchery origin fish recognizable by mark or tag and manner consistent with information representative known fraction of each release group marked or needs and protocols for monitoring tagged uniquely. impacts to natural- and hatchery- 3.1.2. Number of unique marks recovered per monitoring stratum origin fish at the targeted life sufficient to estimate number of unmarked fish from each stage(s)(e.g. in juvenile migration release group with desired accuracy and precision. corridor, in fisheries, etc.). 3.2.1. Abundance of fish by life stage is monitored annually. 3.2.2. Adult to adult or juvenile to adult survivals are estimated. 3.2.3. Temporal and spatial distribution of adult spawners and rearing 3.2. The current status and trends of juveniles in the freshwater spawning and rearing areas are natural origin populations likely to be monitored. impacted by hatchery production are 3.2.4. Timing of juvenile outmigration from rearing areas and adult monitored. returns to spawning areas are monitored. 3.2.5. Ne and patterns of genetic variability are frequently enough to detect changes across generations. 3.3. Fish for harvest are produced and 3.3.1. Number of fish release by location estimated and in compliance released in a manner enabling with AOPs and US vs. OR Management Agreement. effective harvest, as described in all 3.3.2. Number if adult returns by release group harvested applicable fisheries management 3.3.3. Number of non-target species encountered in fisheries for

plans, while avoiding over-harvest of targeted release group. non-target species. 3.4.1. Strays from a hatchery program (alone, or aggregated with 3.4. Effects of strays from hatchery strays from other hatcheries) do not comprise more than 10% of programs on non-target the naturally spawning fish in non-target populations. (unsupplemented and same species) 3.4.2. Hatchery strays in non-target populations are predominately populations remain within acceptable from in-subbasin releases. limits. 3.4.3. Hatchery strays do not exceed 10% of the abundance of any out-of-basin natural population. 3.5.1. Temporal and spatial trends in habitat capacity relative to

3.5. Habitat is not a limiting factor for the spawning and rearing for target population. SUPPLEMENTATIONPROGRAMS HATCHERY EFFECTIVENESSMONITORING REGIONAL FOR AUGMENTATION AND affected supplemented population at 3.5.2. Spatial and temporal trends among adult spawners and rearing juvenile fish in the available habitat. the targeted level of 3. supplementation.

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Category Standards Indicators

3.6.1. Pre- and post-supplementation trends in abundance of fish by life stage is monitored annually. 3.6. Supplementation of natural 3.6.2. Pre- and post-supplementation trends in adult to adult or population with hatchery origin juvenile to adult survivals are estimated. production does not negatively 3.6.3. Temporal and spatial distribution of natural origin and hatchery impact the viability of the target origin adult spawners and rearing juveniles in the freshwater population. spawning and rearing areas are monitored. 3.6.4. Timing of juvenile outmigrations from rearing area and adult returns to spawning areas are monitored. 3.7.1. Adult progeny per parent (P:P) ratios for hatchery-produced fish significantly exceed those of natural-origin fish. 3.7.2. Natural spawning success of hatchery-origin fish must be similar to that of natural-origin fish. 3.7. Natural production of target 3.7.3. Temporal and spatial distribution of hatchery-origin spawners in population is maintained or nature is similar to that of natural-origin fish. enhanced by supplementation. 3.7.4. Productivity of a supplemented population is similar to the natural productivity of the population had it not been supplemented (adjusted for density dependence). 3.7.5. Post-release life stage-specific survival is similar between hatchery and natural-origin population components. 3.8.1. Adult life history characteristics in supplemented or hatchery 3.8. Life history characteristics and influenced populations remain similar to characteristics patterns of genetic diversity and observed in the natural population prior to hatchery influence. variation within and among natural 3.8.2. Juvenile life history characteristics in supplemented or hatchery populations are similar and do not influenced populations remain similar to characteristics in the change significantly as a result of natural population those prior to hatchery influence. hatchery augmentation or 3.8.3. Genetic characteristics of the supplemented population remain supplementation programs. similar (or improved) to the unsupplemented populations. 3.9.1. Genetic characteristics of hatchery-origin fish are similar to 3.9. Operate hatchery programs so that natural-origin fish. life history characteristics and genetic 3.9.2. Life history characteristics of hatchery-origin adult fish are diversity of hatchery fish mimic similar to natural-origin fish. natural fish. 3.9.3. Juvenile emigration timing and survival differences between hatchery and natural-origin fish are minimized. 3.10. The distribution and incidence of 3.10. Detectable changes in rate of occurrence and spatial distribution diseases, parasites and pathogens in of disease, parasite or pathogen among the affected hatchery natural populations and hatchery and natural populations. populations are known and releases of hatchery fish are designed to minimize potential spread or amplification of diseases, parasites, or pathogens among natural populations.

4.1. Artificial production facilities are 4.1.1. Annual reports indicating level of compliance with applicable

operated in compliance with all standards and criteria. applicable fish health guidelines and 4.1.2. Periodic audits indicating level of compliance with applicable facility operation standards and standards and criteria. protocols such as those described by IHOT, PNFHPC, the Co-Managers of Washington Fish Health Policy, INAD, and MDFWP. 4.2.1. Discharge water quality compared to applicable water quality 4.2. Effluent from artificial production standards and guidelines, such as those described or required by facility will not detrimentally affect NPDES, IHOT, PNFHPC, and Co-Managers of Washington Fish natural populations. Health Policy tribal water quality plans, including those relating to temperature, nutrient loading, chemicals, etc. 4.3.1. Water withdrawals compared to applicable passage criteria. 4.3. Water withdrawals and instream 4.3.2. Water withdrawals compared to NMFS, USFWS, and WDFW water diversion structures for juvenile screening criteria. artificial production facility operation 4.3.3. Number of adult fish aggregating and/or spawning immediately will not prevent access to natural below water intake point. spawning areas, affect spawning OPERATIONOFARTIFICIAL PRODUCTION FACILITIES 4.3.4. Number of adult fish passing water intake point. behavior of natural populations, or

4.3.5. Proportion of diversion of total stream flow between intake and

4. impact juvenile rearing environment. outfall.

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Category Standards Indicators

4.4. Releases do not introduce pathogens 4.4.1. Certification of juvenile fish health immediately prior to release, not already existing in the local including pathogens present and their virulence. populations, and do not significantly 4.4.2. Juvenile densities during artificial rearing. increase the levels of existing 4.4.3. Samples of natural populations for disease occurrence before pathogens. and after artificial production releases. 4.5. Any distribution of carcasses or other 4.5.1. Number and location(s) of carcasses or other products products for nutrient enhancement is distributed for nutrient enrichment. accomplished in compliance with 4.5.2. Statement of compliance with applicable regulations and appropriate disease control guidelines. regulations and guidelines, including state, tribal, and federal carcass distribution guidelines. 4.6. Adult broodstock collection operation 4.6.1. Spatial and temporal spawning distribution of natural does not significantly alter spatial and population above and below weir/trap, currently and compared temporal distribution of any naturally to historic distribution. produced population. 4.7. Weir/trap operations do not result in 4.7.1. Mortality rates in trap. significant stress, injury, or mortality 4.7.2. Prespawning mortality rates of trapped fish in hatchery or after in natural populations. release. 4.8. Predation by artificially produced fish 4.8.1. Size at, and time of, release of juvenile fish, compared to size on naturally produced fish does not and timing of natural fish present. significantly reduce numbers of 4.8.2. Number of fish in stomachs of sampled artificially produced fish, natural fish. with estimate of natural fish composition. 5.1. Cost of program operation does not 5.1.1. Total cost of program operation. exceed the net economic value of 5.1.2. Sum of ex-vessel value of commercial catch adjusted fisheries in dollars per fish for all appropriately, appropriate monetary value of recreational fisheries targeting this population. effort, and other fishery related financial benefits. 5.2. Juvenile production costs are 5.2.1. Total cost of program operation.

comparable to or less than other 5.2.2. Average total cost of activities with similar objectives.

ECONOMIC - TIVENESS regional programs designed for

similar objectives. EFFEC SOCIO 5.3. Non-monetary societal benefits for 5.3.1. Number of adult fish available for tribal ceremonial use.

which the program is designed are 5.3.2. Recreational fishery angler days, length of seasons, and number 5. achieved. of licenses purchased.

1.11 EXPECTED SIZE OF PROGRAM

1.11.1Proposed annual broodstock collection level (maximum number of adult fish)

The current spring/summer Chinook salmon program at the Clearwater Hatchery includes the release of 2,635,000 spring-run Chinook salmon and 200,000 summer-run Chinook salmon. To achieve these release goals, approximately 950 spring-run and 60 summer-run females are collected for broodstock and a similar number of males are collected. Additionally, IDFG provides eggs from up to 200 females to the Nez Perce Tribe for programs operated in the Clearwater River drainage.

South Fork Clearwater River Program – Red River and Crooked River traps (IDFG mitigation program): Approximate adult spawn target: 470 females (approximately 1.88 million green eggs).

South Fork Clearwater River Program – Red River and Crooked River traps (Nez Perce Tribal supplementation program): The Nez Perce Tribe requests eggs from up to 200 females.

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Lochsa River Program – Powell trap (IDFG mitigation program): Approximate adult spawn target: 483 females (approximately 1.94 million eggs).

1.11.2 Proposed annual fish release levels (maximum number) by life stage and location

Information presented in Table 2 was taken from the brood year 2004 IDFG spring Chinook salmon mark plan. Generally, the number of adipose fin-clipped juvenile salmon is relatively stable from year-to-year. However, the number of fish dedicated to other management objectives may vary from year-to-year.

Table 2. Location and life stage of Chinook salmon released from the Clearwater Fish Hatchery.

LIFE STAGE and RUN RELEASE TYPE LOCATION ANNUAL RELEASE LEVEL Eyed Eggs 0 Unfed Fry 0 Fry 0 (Parr) Upper Selway Fingerling (Spring CH) 300,000 No clip/OTC mark River Yearlings Transfer to NPTH 200K; 66K Ad/CWT, 134K CWT only 400K; 145K AD, 120K Ad/CWT, 135K CWT only, Lower Selway River Full Term Smolt (Spring CH) 17,100 PIT Crooked River Release moved to Red River to accommodate Full Term Smolt (Spring CH) Summer CH run at Crooked River Full Term Smolt (Spring CH) Red River 1.1 Mil; 100% Ad, 120K Ad/CWT, 21,500 PIT Full Term Smolt (Spring CH) Powell 400K; 100% Ad, 120K Ad/CWT, 17,100 PIT Full Term Smolt (Spring CH) Clear Creek 235K; 100% Ad, 120K Ad/CWT, 17,100 PIT Full Term Smolt (Summer CH) Lower Crooked River 200-1,000K; 100% CWT No Ad clip. In the future ad clip will be added when run is self supporting Note: the following abbreviations are used in the table: NPT supplementation = Nez Perce Tribe Supplementation Studies ISS = Idaho Supplementation Studies NPTH = Nez Perce Tribal Hatchery LSRCP = Lower Snake River Compensation Program

1.12 CURRENT PROGRAM PERFORMANCE, INCLUDING ESTIMATED SMOLT-TO-ADULT SURVIVAL RATES, ADULT PRODUCTION LEVELS, AND ESCAPEMENT LEVELS. INDICATE THE SOURCE OF THESE DATA.

The most recent Idaho Department of Fish and Game performance data for Powell, Red River, and Crooked River satellite facilities are presented in tables 3 and 4. For some years, no harvest estimates were generated from Columbia and Snake river fisheries. As such, the SAR information presented below are minimum estimates for those years. Page 14

Table 3. Clearwater Fish Hatchery Chinook salmon smolt-to-adult return (SAR) and smolt-to-adult survival (SAS) rates and escapement data for adipose clipped yearling smolts released at the Powell satellite Facility 1994-2006. Total SAS includes fish harvested or recovered below Lower Granite Dam (LGD)

Release Return Number of Escapement to SAR to Total Fish Total Year Years Smolts Released LGD LGD Produced SAS 2006 07-09 423,633 1,804 0.43% 3,464 0.82% 2005 06-08 403,917 1,355 0.34% 1,590 0.39% 2004* 05-07 376,797 512 0.14% 526 0.14% 2003* 04-06 350,665 370 0.11% 370 0.11% 2002* 03-05 349,890 2,597 0.74% 2,625 0.75% 2001* 02-04 212,648 1,139 0.54% 1,211 0.57% 2000 01-03 293,522 2,308 0.79% 3,411 1.16% 1999 00-02 334,477 2,989 0.89% 4,272 1.28% 1998 99-01 244,847 2,292 0.94% 2,373 0.97% 1997* 98-00 3,513 28 0.80% 28 0.80% 1996 97-99 232,731 242 0.10% 257 0.11% 1995 96-98 290,417 927 0.32% 1,001 0.34% 1994 95-97 200,568 263 0.13% 284 0.14% Geometric Mean 0.36% 0.42% *Release group was not represented with CWT so harvest in the Columbia and Snake rivers is not accounted for.

Table 4. Clearwater Fish Hatchery Chinook salmon smolt-to-adult return (SAR) and smolt-to-adult survival (SAS) rates and escapement data for adipose clipped yearling smolts released at the Red and Crooked River satellite facilities 1994-2006. Total SAS includes fish harvested or recovered below Lower Granite Dam (LGD)

Release Return Number of Smolts Escapement to SAR to Total Fish Total Year Years Released LGD LGD Produced SAS 2006 07-09 1,173,064 3,382 0.29% 5,496 0.47% 2005 06-08 1,101,749 1,087 0.10% 1,350 0.12% 2004* 05-07 1,105,185 1,652 0.15% 1,696 0.15% 2003* 04-06 980,753 679 0.07% 768 0.08% 2002* 03-05 1,076,807 2,547 0.24% 2,649 0.25% 2001* 02-04 38,943 323 0.83% 323 0.83% 2000 01-03 555,061 3,754 0.68% 5,172 0.93% 1999* 00-02 961,964 7,326 0.76% 8,881 0.92% 1998* 99-01 205,906 2,069 1.00% 2,117 1.03% 1997* 98-00 2,970 37 1.25% 37 1.25% 1996* 97-99 61,073 174 0.28% 189 0.31% 1995 96-98 537,908 1,372 0.26% 1,441 0.27% 1994 95-97 273,766 255 0.09% 274 0.10% Geometric Mean 0.31% 0.35% *Release group was not represented with CWT so harvest in the Columbia and Snake rivers is not accounted for.

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1.13 DATE PROGRAM STARTED (YEARS IN OPERATION)

The Clearwater Fish Hatchery was completed and became operational in the fall of 1991. Completion dates of the satellite facilities are: Powell – 1989, Red River - 1976, and Crooked River - 1990. The Red River facility was originally constructed in 1976 under the Columbia Basin Development Program and was modified in 1986 under the Lower Snake River Compensation Program.

1.14 EXPECTED DURATION OF PROGRAM

This program is expected to continue indefinitely to provide mitigation under the Lower Snake River Compensation Plan.

1.15 WATERSHEDS TARGETED BY PROGRAM

Listed by hydrologic unit code –

Clearwater River, Idaho: 17060306 South Fork Clearwater River: 17060305 Lochsa River: 17060303

1.16 INDICATE ALTERNATIVE ACTIONS CONSIDERED FOR ATTAINING PROGRAM GOALS

As mentioned earlier, the Clearwater Fish Hatchery was constructed to mitigate for fish losses caused by construction and operation of the four lower Snake River federal hydroelectric dams. The Clearwater Fish Hatchery has a federally authorized goal of returning 12,000 adult spring Chinook salmon to reaches upstream of Lower Granite Dam after a harvest of 48,000. The Idaho Department of Fish and Game’s objective is to ensure that harvestable components of hatchery- produced Chinook salmon are available to provide fishing opportunities, consistent with meeting spawning escapement and preserving the genetic integrity of natural populations (IDFG 1992).

This mitigation program has never achieved the escapement goal of 12,000 adults to Lower Granite Dam since the inception of the program. Based on the most recent 10 year geometric mean SAR of 0.34% to Lower Granite dam, the production capacity at this facility needs to be increased to 3.5 million yearling smolts to return 12,000 adults to the project area under current Columbia River harvest schedules.

Early in the program, managers agreed (through the USvOR process) to scale back the steelhead production goals that were originally modeled for the program to meet the mitigation goal of returning 14,000 steelhead back to Lower Granite Dam. This reduction in steelhead production left vacant rearing space at Clearwater Fish Hatchery. Managers have prioritized the use of that space to increase the production of spring and summer run Chinook salmon at Clearwater Fish Hatchery.

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The original production target for spring Chinook salmon was 1.4 million yearling smolts. Currently, 2,135,000 yearling spring Chinook smolts are reared at Clearwater Fish Hatchery. All but 135,000 of these are adipose fin clipped. Additionally, 500,000 subyearling spring Chinook salmon are released at Clearwater Fish Hatchery.

In addition to the existing the spring Chinook program, managers are developing a locally adapted summer-run Chinook population in the Clearwater River. Anecdotal accounts of wild Chinook returns to Clearwater basin prior to their extirpation suggest that they may have included both spring and summer run populations. IDFG, the Nez Perce Tribe, and the LSRCP initiated a program in 2009 to evaluate the possibility of building a locally adapted hatchery in the Clearwater River drainage. Eggs from the harvest portion of the McCall Hatchery summer run Chinook salmon program on the South Fork Salmon River are being incubated and reared at the Clearwater Fish Hatchery. The smolts will be released in the Crooked River in the upper South Fork Clearwater drainage. Adult returns from those releases will be trapped at the Crooked River trapping facility and used to develop a locally adapted and fully independent summer run broodstock for subsequent harvest and supplementation releases in the Selway and South Fork Clearwater rivers. Egg transfers from the McCall Hatchery will cease once a locally adapted broodstock is developed. Currently, Clearwater Fish Hatchery is rearing 200,000 summer run Chinook salmon with the eventual goal of releasing 1,000,000 summer run yearling Chinook Salmon. Once this goal is reached, Clearwater Fish Hatchery will be releasing 3,135,000 yearling, and 500,000 subyearling Chinook salmon. Once the summer run broodstock is established, the long term goal is to move the summer run program to the Selway River. In order to accomplish this, a broodstock collection facility will be needed in the Selway River drainage.

This HGMP does not reflect the facility and personnel needs that would be required to fully develop the one million summer-run Chinook salmon smolt program. Instead, this HGMP addresses needs to operate the program under status quo as described in the Executive Summary. This includes maintaining 2,135,000 spring run yearling smolts and 500,000 sub-yearling spring run Chinook Salmon and 200,000 yearling summer-run Chinook salmon.

It should be noted that a significant proportion of the natural production monitoring conducted by IDFG that occurs in the upper South Fork Clearwater River and upper Lochsa River is funded through an ongoing BPA funded supplementation research project (Bowles and Leitzinger 1991, BPA Project Number: 1989-098-00). This project is expected to sunset in 2014 and in order to continue monitoring the natural population in these areas, additional funds will be required.

Recommendations from the USFWS Hatchery Review Team (HRT) Recommendations

The HRT provided several potential programmatic alternatives to the current hatchery program along with their recommendation for the preferred alternative. For the Clearwater Fish Hatchery spring Chinook salmon program, the HRT preferred alternative is for the managers to shift a component of production releases to the North Fork Clearwater River and reduce the releases in the Lochsa and South Fork Clearwater rivers. In the short term the focus would be to develop integrated/conservation broodstocks in these areas. In the long term, the focus would shift to developing stepping stone broodstocks in an attempt to shift mitigation production back to the Lochsa and South Fork Clearwater rivers.

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Managers considered all the alternatives presented by the HRT and believe that the segregated program does not pose significant risk to the natural populations in the Clearwater drainage. In addition , natural populations in the Clearwater River are not part of the Snake River spring/summer Chinook salmon ESU and current natural populations are a direct result of the hatchery program. Managers will continue to implement best management practices associated with operation of the hatcheries and restoration of natural populations.

In addition to the programmatic recommendations, the review team also provided specific recommendations across eight categories: Program Goals and Objectives; Broodstock Choice and Collection; Hatchery and Natural Spawning; Incubation and Rearing; Release and Outmigration; Facilities and Operations; Research, Monitoring and Accountability; and Education and Outreach. Reponses from the managers for each of the recommendations are provided in Appendix B.

SECTION 2. PROGRAM EFFECTS ON NMFS ESA-LISTED SALMONID POPULATIONS

2.1 LIST ALL ESA PERMITS OR AUTHORIZATIONS IN HAND FOR THE HATCHERY PROGRAM

Section 7 consultation with U.S. Fish and Wildlife Service (April 2, 1999) resulting in NMFS Biological Opinion for the Lower Snake River Compensation Program.

2.2 PROVIDE DESCRIPTIONS, STATUS, AND PROJECTED TAKE ACTIONS AND LEVELS FOR NMFS ESA-LISTED NATURAL POPULATIONS IN THE TARGET AREA

2.2.1 Description of NMFS ESA-listed salmonid population(s) affected by the program

No wild/natural, ESA-listed spring Chinook salmon adults or juveniles are collected or directly affected as part of the Clearwater Fish Hatchery mitigation program described in this HGMP.

The following information on the present status of Clearwater River basin spring Chinook salmon was taken from the Draft Clearwater Subbasin Summary for the Clearwater Subbasin of the Mountain Snake Province (NPPC 2001).

Indigenous Chinook salmon in the Clearwater River subbasin were eliminated by Lewiston Dam (Schoen et al. 1999; Murphy and Metsker 1962). However, naturalized populations of spring Chinook salmon have been re-established in some portions of the subbasin as a result of reintroduction efforts (Schoen et al. 1999; Larson and Mobrand 1992).

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Spring Chinook salmon within the Clearwater subbasin are excluded from the ESU encompassing other spring/summer stocks throughout the Snake River basin, but represent an important effort aimed at restoring an indigenous fish population to an area from which they had been extirpated. Efforts to reestablish spring Chinook salmon in the subbasin were extensive and have previously been summarized by Nez Perce Tribe and Idaho Department of Fish and Game (1990), Cramer and Neeley (1992), and Cramer (1995), and Bowles and Leitzinger (1991). Currently hatchery spring Chinook are released for harvest mitigation and to supplement natural production (Nez Perce Tribe and Idaho Department of Fish and Game 1990; Idaho Department of Fish and Game 2001).

Reintroduction of spring Chinook salmon following removal of the Lewiston Dam has resulted in naturally reproducing runs in Lolo Creek, and mainstems and tributaries of the Lochsa, Selway, and South Fork Clearwater Rivers (Larson and Mobrand 1992). Founding hatchery stocks used for spring Chinook salmon reintroductions were primarily obtained from the Rapid River Hatchery (Kiefer et al. 1992; Nez Perce Tribe and Idaho Department of Fish and Game 1990). Initially however, spring Chinook stocks imported for restoration came from Carson, Big White, Little White or other spring Chinook captured at Bonneville Dam (Nez Perce Tribe and Idaho Department of Fish and Game 1990). Genetic analyses confirm that existing natural spring Chinook salmon in the Clearwater River subbasin are derived from reintroduced Snake River stocks (Matthews and Waples 1991).

Spring Chinook salmon enter the Columbia River and begin spawning migrations during April and May, reaching the Clearwater subbasin from April through July (Nez Perce Tribe and Idaho Department of Fish and Game 1990). Spring Chinook salmon indigenous to the Snake River basin tend to spawn earlier and higher in elevation than summer (early-fall) and fall races (Chapman et al. 1991). Spawning of spring stocks typically occurs in tributaries and headwater streams in August and September. Eggs hatch in December with emergence complete by April (Nez Perce Tribe and Idaho Department of Fish and Game 1990; U.S. Fish and Wildlife Service 1999). Spring Chinook salmon remain in freshwater for one year, migrating to the ocean in the spring of their second year, typically from March through June (U.S. Fish and Wildlife Service 1999; Walters et al. 2001). Nearly all adult spring and summer Chinook that return to the Snake River basin result from fish that smolted as yearlings in April-May (Matthews and Waples 1991).

Although spring Chinook salmon smolt as yearlings, in-basin migrations as fry or parr are not uncommon. Fry dispersal was well documented in the Selway River during studies of Chinook salmon reintroductions (Cramer 1995). A second downstream migration of spring Chinook salmon in the upper portion of the rearing areas occurs in the fall as juveniles seek suitable winter habitat (Hesse et al. 1995; Walters et al. 2001).

Little is known about the distribution of Snake River spring Chinook salmon in the ocean because few are ever caught in ocean fisheries. Analyses of coded-wire tag (CWT) recoveries from Snake River spring Chinook salmon during the intensive ocean fisheries of the 1980s indicated that harvest rate of these fish in the ocean was less than 1% (Berkson 1991).

Distribution of spring Chinook salmon to the North Fork Clearwater River is blocked by Dworshak Dam, and with the exception of the mainstem migration corridor, they are absent from the Lower Clearwater. The current distribution of spring Chinook salmon within the Clearwater

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subbasin includes the Lolo Creek drainage and all major drainages above the confluence of the Middle and South Forks of the Clearwater River. Relatively contiguous distributions of spring/summer Chinook salmon exist in the Lolo/Middle Fork, South Fork, and Upper and Lower Selway. Spring/summer Chinook salmon are absent from many tributaries in the Lochsa River drainage, but found in Pete King and Fish Creeks, and most tributaries above (and including) Warm Springs Creek.

Spring Chinook salmon are classified as “present – depressed” in all areas of the Clearwater subbasin where status information is available. Aerial surveys of spring Chinook salmon redds in the Clearwater subbasin have been conducted since 1966. Data has been collected from established reaches on an annual basis in both natural production areas as well as areas where production is regularly influenced by hatchery releases of Chinook salmon.

Adult Run Timing - Run timing of natural-origin adults returning to the Powell and South Fork Clearwater traps generally occurs between late May and early September and resembles a bimodal distribution that is heavily skewed toward the first mode. The dates at which the 25th, 50th, and 75th percentiles of adults returning to the traps are displayed in Table 5 below.

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Table 5. Timing of adult returns to the Powell and South Fork Clearwater rivers, 1998-2008. Number of Proportion of Returning Adults Weir Return Year Natural Origin Returns 25% 50% 75% Powell / Crooked Fork 1998 19 4-Jul 24-Aug 2-Sep Powell / Crooked Fork 1999 9 31-Jul 22-Aug 25-Aug Powell / Crooked Fork 2000 55 26-Jun 4-Jul 21-Aug Powell / Crooked Fork 2001 259 27-Jun 5-Jul 23-Aug Powell / Crooked Fork 2002 50 22-Jun 24-Jun 26-Jun Powell / Crooked Fork 2003 86 26-Jun 10-Jul 14-Jul Powell / Crooked Fork 2004 109 1-Jul 16-Jul 21-Aug Powell / Crooked Fork 2005 35 6-Jul 23-Jul 23-Aug Powell / Crooked Fork 2006 39 24-Jun 28-Jun 2-Jul Powell / Crooked Fork 2007 21 16-Jun 24-Jun 2-Jul Powell / Crooked Fork 2008 37 22-Jul 27-Jul 19-Aug

Number of Proportion of Returning Adults Weir Return Year Natural Origin Returns 25% 50% 75% Crooked River 1998 43 22-Jun 1-Jul 7-Jul Crooked River 1999 4 9-Jul 12-Jul 15-Jul Crooked River 2000 74 22-Jun 3-Jul 3-Sep Crooked River 2001 364 19-Jun 26-Jun 5-Jul Crooked River 2002 170 26-Jun 30-Jun 11-Jul Crooked River 2003 219 19-Jun 24-Jun 1-Jul Crooked River 2004 97 24-Jun 26-Jun 7-Jul Crooked River 2005 23 22-Jun 23-Jun 23-Jul Crooked River 2006 8 22-Jun 24-Jun 27-Jun Crooked River 2007 13 14-Jun 27-Jun 14-Jul Crooked River 2008 61 5-Jul 11-Jul 26-Aug

Number of Proportion of Returning Adults Weir Return Year Natural Origin Returns 25% 50% 75% Red River 1998 25 19-Jun 27-Jun 11-Jul Red River 1999 9 11-Jul 14-Jul 25-Aug Red River 2000 51 16-Jun 22-Jun 26-Jun Red River 2001 527 19-Jun 26-Jun 13-Aug Red River 2002 104 23-Jun 28-Jun 7-Jul Red River 2003 41 20-Jun 21-Jun 29-Jun Red River 2004 26 22-Jun 24-Jun 27-Jun Red River 2005 12 22-Jun 23-Jun 24-Jun Red River 2006 37 22-Jun 25-Jun 27-Jun Red River 2007 21 22-Jun 22-Jun 23-Jun Red River 2008 51 7-Jul 11-Jul 13-Aug

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120% Hatchery 100% Natural

80%

60%

40%

20%

0%

6/7 7/2 8/1 8/6 7/7 9/5

5/31 6/12 6/22 6/27 7/12 7/17 7/22 8/11 8/21 8/26 8/31 9/10 6/17 7/27 8/16

Figure 1. Cumulative proportion of hatchery- and natural-origin Chinook salmon arrivign at the Powell satellite facility adult trap (average value from 1997-2008).

120% Hatchery 100% Natural

80%

60%

40%

20%

0%

6/5 7/5 8/4 9/3 9/8 8/9

5/26 6/10 6/15 6/25 7/15 7/25 8/14 8/19 8/24 8/29 9/13 6/20 6/30 7/10 7/20 7/30

Figure 2. Cumulative proportion of hatchery- and natural-origin Chinook salmon arriving at the Red River and Crooked River (combined) satellite facilities (average value from 1997-2008).

Adult Age Structure – Spring- and summer-run Chinook salmon in the Snake River ESU are comprised of four age classes (1, 2, 3, and 4 ocean) with the majority returning after two or three years in the ocean (Table 6). Using dorsal fin ray aging techniques, Keifer et al (2002, 2004) and Copeland et al. (2008) estimated the ocean age proportions of natural-origin spring/summer run

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Chinook salmon passing upstream of Lower Granite Dam from 2002 through 2007. They found that, while age structure was variable from year to year, the majority of returning adults were composed of two-ocean adults.

Table 6. Estimated percent by age class of wild Chinook salmon passing Lower Granite Dam 2002-2007. Return Year 1-Ocean 2-Ocean 3-Ocean 4-Ocean 2002 1.2 52.8 45.0 1.0 2003 7.0 19.9 70.7 1.9 2004 5.9 84.2 9.7 0.2 2005 7.0 66.3 25.7 1.0 2006 3.5 79.5 17.0 0.0 2007 14.1 45.4 38.7 1.7 Source: Copeland et al. 2008

Ages of natural-origin Chinook salmon returning to the Clearwater n River weir are determined based on length frequency and consist of three age classes (1, 2, and 3 ocean). While it is likely that a few four-ocean adults return to the Clearwater River, overlapping length frequencies of three- and four-ocean adults precludes being able to distinguish the two age classes based on length frequency alone. Age class structure of natural-origin adults returning to the Powell, Crooked River and Red River satellite facilities from 1998-2008 are displayed in tables 7, 8, and 9 below.

Table 7. Age class structure (percent in each age class) of natural-origin Chinook salmon captured at the Powell Satellite. Return Year No. of Natural Adults 1-Ocean 2-Ocean 3-Ocean 1998 25 0.0 25.0 75.0 1999 9 20.0 40.0 40.0 2000 51 23.1 76.9 0.0 2001 527 0.5 93.0 6.5 2002 104 0.0 60.6 39.4 2003 41 2.7 8.1 89.2 2004 26 12.5 79.2 8.3 2005 12 16.7 75.0 8.3 2006 37 3.7 88.9 7.4 2007 21 28.6 57.1 14.3 2008 54 16.7 77.8 5.5 Average 11.3 62.0 26.7

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Table 8. Age class structure (percent in each age class) of natural-origin Chinook salmon captured at the Crooked River Satellite Facility. Return Year No. of Natural Adults 1-Ocean 2-Ocean 3-Ocean 1998 43 0.0 37.5 62.5 1999 4 0.0 25.0 75.0 2000 74 35.2 64.8 0.0 2001 364 0.7 94.4 4.9 2002 170 7.8 52.1 40.1 2003 219 1.8 48.2 50.0 2004 97 18.5 79.4 2.1 2005 23 26.1 60.9 13.0 2006 8 16.7 83.3 0.0 2007 13 30.8 61.5 7.7 2008 61 24.6 63.9 11.5 Average 14.7 61.0 24.3 Table 9. Age class structure (percent in each age class) of natural-origin Chinook salmon captured at the Red River Satellite Facility. Return Year No. of Natural Adults 1-Ocean 2-Ocean 3-Ocean 1998 25 0.0 25.0 75.0 1999 9 20.0 40.0 40.0 2000 51 23.1 76.9 0.0 2001 527 0.5 93.0 6.5 2002 104 0.0 60.6 39.4 2003 41 2.7 8.1 89.2 2004 26 12.5 79.2 8.3 2005 12 16.7 75.0 8.3 2006 37 3.7 88.9 7.4 2007 21 28.6 57.1 14.3 2008 54 16.7 77.8 5.5 Average 11.3 62.0 26.7 Size Range of Returning Adults - Natural-origin adults returning to the Clearwater River (Powell, Red River, and Crooked River trap sites) generally range in size from 50-110 cm fork length. The majority of adult returns are in the 70-90 cm size class but vary depending on year class strength. Typically, one-ocean adults are less than 63cm fork length, two-ocean fish are 63-85 cm and three-ocean fish are greater than 85 cm (IDFG, unpublished data). The tables (10, 11, and 12) below display the number, in each ten millimeter size class, of natural-origin Chinook salmon captured at the Powell, Crooked River, and Red River satellite facilities from 2001 through 2008.

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Table 10. Number of natural-origin Chinook salmon returning to the Powell satellite facility in each 10mm length group 2001-2008.

Adult Return Year Fork Length (cm) 2001 2002 2003 2004 2005 2006 2007 2008 <50 0 1 1 0 0 0 2 1 50-59 4 0 2 0 1 0 3 4 60-69 27 2 5 28 8 8 2 4 70-79 190 25 32 56 17 27 4 14 80-89 35 21 19 16 6 2 7 11 90-99 2 1 17 5 3 2 3 3 100-109 1 0 10 0 0 0 0 0 110-119 0 0 0 0 0 0 0 0 Total 259 50 86 105 35 39 21 37 Source: IDFG Hatchery Brood Reports and unpublished data Table 11. Number of natural-origin Chinook salmon returning to the Crooked River satellite facility in each 10mm length group 2001-2008 (IDFG Hatchery Brood Reports and unpublished data).

Adult Return Year Fork Length (cm) 2001 2002 2003 2004 2005 2006 2007 2008 <50 1 7 1 0 4 0 1 1 50-59 1 6 3 1 0 0 3 8 60-69 30 5 5 32 5 2 1 10 70-79 260 63 90 57 9 4 5 30 80-89 72 62 61 6 5 2 3 6 90-99 0 25 51 0 0 0 0 5 100-109 0 2 8 1 0 0 0 1 110-119 0 0 0 0 0 0 0 0 Total 364 170 219 97 23 8 13 61 Source: IDFG Hatchery Brood Reports and unpublished data Table 12. Number of natural-origin Chinook salmon returning to the Red River satellite facility in each 10mm length group 2001-2008.

Adult Return Year Fork Length (cm) 2001 2002 2003 2004 2005 2006 2007 2008 <50 0 0 0 0 0 0 1 0 50-59 2 0 1 1 0 0 3 5 60-69 38 11 1 7 2 8 3 11 70-79 378 47 6 14 7 21 4 30 80-89 101 32 20 4 3 8 8 6 90-99 8 12 11 0 0 0 2 2 100-109 0 2 2 0 0 0 0 0 110-119 0 0 0 0 0 0 0 0 Total 527 104 41 26 12 37 21 54 Source: IDFG Hatchery Brood Reports and unpublished data

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Adult Sex Ratio – The sex ratio of natural-origin adults at the Powell, Crooked River and Red River adult traps varies from year to year, but is generally skewed towards males. The average percent of adult returns composed of males from 1996-2008 is displayed in tables 13, 14, and 15 below.

Table 13. Percent of natural-origin Chinook salmon returns to the Powell satellite weir that was composed of males 1996-2008.

Percent of natural-origin return Return Year Jacks Included Jacks Excluded 1996 100.0 100.0 1997 100.0 100.0 1998 73.7 73.7 1999 57.1 25.0 2000 73.8 63.9 2001 68.2 66.5 2002 70.3 70.3 2003 57.8 55.7 2004 53.2 50.0 2005 65.5 65.5 2006 63.3 60.7 2007 No Gender for Released Fish 2008 82.6 78.9 Average 72.1 67.5 Source: IDFG unpublished data Table 14. Percent of natural-origin Chinook salmon returns to the Crooked River satellite weir that was composed of males 1996-2008.

Percent of natural-origin return Return Year Jacks Included Jacks Excluded 1996 68.9 66.7 1997 45.6 45.6 1998 27.5 27.5 1999 75.0 75.0 2000 82.4 72.8 2001 47.7 47.3 2002 56.3 52.6 2003 42.2 41.1 2004 67.0 59.5 2005 65.2 52.9 2006 50.0 40.0 2007 No Gender for Released Fish 2008 68.0 60.0 Average 58.0 53.4 Source: IDFG unpublished data Page 26

Table 15. Percent of natural-origin Chinook salmon returns to the Red River satellite weir that was composed of males 1996-2008.

Percent of natural-origin return Return Year Jacks Included Jacks Excluded 1996 93.3 91.7 1997 48.6 47.2 1998 33.3 33.3 1999 80.0 75.0 2000 84.6 80.0 2001 50.2 49.9 2002 54.3 54.3 2003 40.5 38.9 2004 66.7 61.9 2005 58.3 50.0 2006 55.6 53.8 2007 No Gender for Released Fish 2008 72.2 68.8 Average 61.5 58.7 Source: IDFG unpublished data Juvenile Life History and Migration Timing – Juvenile trapping data collected from the Crooked Fork Creek screw trap (Figure 3) in the upper Lochsa River indicates that the majority of juvenile Chinook emigrate from the spawning area as sub-yearling parr and pre-smolts during summer and fall with a small component of yearling smolts migrating the following spring. The trap is typically operated from March through October, so fish emigrating between November and February are not accounted for. Also, for most years, the trap is not operated for a one to three week period during spring high flows in May and June. Trapping data from the South Fork Clearwater River (Red and Crooked River) shows a similar pattern.

Regardless of when juveniles emigrate from the spawning areas in the Clearwater River, they rear in fresh water for one full year after emergence and subsequently migrate to the ocean as yearling smolts from April through June. Table 16 below shows the seaward migration timing of natural-origin Chinook salmon from Crooked Fork Creek and Red River based on PIT-tag interrogation data from Lower Granite Dam for brood years 1997-2007. Fish were PIT-tagged as both subyearling parr and pre-smolts and as yearling smolts. Juveniles PIT-tagged as subyearlings typically arrive at Lower Granite Dam three to four weeks prior to juveniles tagged as yearling smolts (Table 16).

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Figure 3. Emigration timing of natural-origin Chinook salmon at the Crooked Fork Creek screw trap BY 2002-2007 (IDFG unpublished data).

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Table 16. Number (N) of PIT-tagged natural-origin juvenile Chinook salmon detected at Lower Granite Dam and the dates at which the first and last fish were detected and the dates at which 10%, 50%, and 90% were detected. BY Stage N MIN 10% 50% 90% MAX 2007 S 133 4/2 4/18 5/8 5/29 6/16 Y 28 4/29 5/6 5/20 6/14 6/20 2006 S 158 4/1 4/23 5/9 6/12 7/4 Y 22 5/6 5/11 6/2 6/22 7/14 2005 S 81 3/27 4/5 4/23 5/21 6/12 Y 18 5/3 5/9 5/19 6/2 6/11 2004 S 211 3/31 4/19 5/9 6/4 7/6 Y 31 4/12 4/26 5/20 6/18 7/3 2003 S 249 4/11 4/20 5/6 6/2 6/19 Y 86 4/27 5/4 5/23 6/13 6/20 2002 S 322 4/6 4/23 5/7 5/25 6/27

Y 66 4/24 5/4 5/24 6/16 7/5 Crooked Fork Creek Fork Crooked 2001 S 106 3/25 4/22 5/15 6/8 9/28 Y 42 4/26 5/9 6/7 6/23 7/21 2000 S 84 4/2 4/21 5/20 6/17 6/27 Y 22 4/15 5/7 6/14 6/29 6/30 1999 S 189 4/15 5/4 5/23 6/12 7/27 Y 102 4/30 5/12 6/4 6/16 7/16 2007 S 184 4/3 4/16 5/13 6/8 6/24 Y 10 6/20 6/26 7/1 7/8 7/9 2006 S 64 4/17 5/2 5/14 6/19 7/10 Y 26 5/28 6/10 7/3 7/10 8/30 2005 S 15 4/9 4/17 5/13 5/18 5/22 Y 50 5/2 5/12 5/21 6/16 6/20 2004 S 78 4/5 4/17 5/8 6/6 6/21 Y 38 5/19 5/29 6/8 6/19 6/29 2003 S 106 4/9 4/20 5/4 6/6 6/22 Y 437 4/23 5/22 6/8 6/19 7/4 Red River Red 2002 S 91 4/6 4/25 5/12 6/14 7/4 Y 429 5/3 5/23 6/12 7/2 7/31 2001 S 17 4/23 4/25 5/18 6/21 7/2 Y 21 6/3 6/17 6/30 7/18 7/24 2000 S 22 4/10 4/14 5/13 6/23 6/30 Y 121 5/15 6/1 6/24 7/5 7/17 1999 S 72 4/11 4/21 5/4 6/2 7/12 Y 74 4/30 5/20 6/9 7/5 7/19

Source: IDFG unpublished data Note: Y= fish tagged as yearlings ; S=fish tagged as sub-yearlings

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Identify the NMFS ESA-listed population(s) that will be directly affected by the program The operation of the Clearwater Fish Hatchery and its satellite facilities is expected to have no direct affect on ESA-listed species.

Identify the NMFS ESA-listed population(s) that may be incidentally affected by the program Snake River Fall-run Chinook salmon ESU (Threaten – 4/92)

Snake River Spring/Summer-run Chinook salmon ESU (Threaten – 4/92)

Snake River Basin steelhead ESU (Threaten – 8/97)

Bull trout (Threaten – 6/98)

2.2.2 Status of NMFS ESA-listed salmonid population(s) affected by the program

Describe the status of the listed natural population(s) relative to “critical” and “viable” population thresholds Spring Chinook salmon within the Clearwater subbasin are excluded from the ESU that encompasses other Snake River basin spring/summer stocks. No wild/natural, ESA-listed spring Chinook salmon adults or juveniles are collected or directly affected as part of the Clearwater Fish Hatchery mitigation program described in this HGMP.

Provide the most recent 12 year progeny-to-parent ratios, survival data by life-stage, or other measures of productivity for the listed population. Indicate the source of these data Spring Chinook salmon within the Clearwater subbasin are excluded from the ESU that encompasses other Snake River basin spring/summer stocks. No wild/natural, ESA-listed spring Chinook salmon adults or juveniles are collected or directly affected as part of the Clearwater Fish Hatchery mitigation program described in this HGMP.

Provide the most recent 12 year annual spawning abundance estimates, or any other abundance information. Indicate the source of these data. Spring Chinook salmon within the Clearwater subbasin are excluded from the ESU that encompasses other Snake River basin spring/summer stocks. No wild/natural, ESA-listed spring Chinook salmon adults or juveniles are collected or directly affected as part of the Clearwater Fish Hatchery mitigation program described in this HGMP.

Provide the most recent 12 year estimates of annual proportions of direct hatchery-origin and listed natural-origin fish on natural spawning grounds, if known. Spring Chinook salmon within the Clearwater subbasin are excluded from the ESU that encompasses other Snake River basin spring/summer stocks. No wild/natural, ESA-listed spring Chinook salmon adults or juveniles are collected or directly affected as part of the Clearwater Fish Hatchery mitigation program described in this HGMP.

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2.2.3 Describe hatchery activities, including associated monitoring and evaluation and research programs that may lead to the take of NMFS listed fish in the target area, and provide estimated annual levels of take.

Describe hatchery activities that may lead to the take of listed salmonid populations in the target area, including how, where and when the takes may occur, the risk potential for their occurrence, and the likely effects of the take.

Hatchery Operational Activities:

Take of ESA listed anadromous salmonids due to adult trapping and broodstock collection at the Clearwater Fish Hatchery satellite facilities for this program is not anticipated.

Hatchery Programmatic Maintenance Activities at Satellite Facilities

The rivers that supply water to each satellite facility, (Red River, upper and lower Crooked River and Powell), flow through a valley which is heavily influenced by logging and or historic mining activity. The rivers transport and deposit a great deal of sediment which can hamper normal hatchery operation. As such, in-river maintenance of the hatchery diversion dams and intake structures, intake piping, adult fish weir and fish ladder is a common requirement. A description of each maintenance task follows.

Satellite facility diversion dam and water source intake: The various wooden, steel and concrete structures which constitute the diversion dams and water source intakes at both the upper and lower Crooked River facilities, Red River and Powell sites may become compromised simply from age and exposure to changing weather conditions. Hatchery personnel must periodically complete a visual inspection of the structures by entering the river channel with hip boots or waders or dry suits with supplied air systems. Minor repairs such as stop-log replacement or rebuilding of cobble diversion weir at Red River may be completed in place by workers using hand tools, while more extensive repairs may require portions of these structures to be temporarily removed for repair or replacement. Should removal of these structures be necessary, a backhoe/trackhoe or a crane or similar lifting device operated from the stream bank would be employed. Heavy equipment will not enter the stream channel. In some instances it may be necessary to construct a small cofferdam to isolate the work area from the river to facilitate repair work. Cofferdams would be constructed from sheet piling or ecology blocks lined with heavy mil plastic sheeting, thereby reducing the potential for sediment to escape and be transported downstream. Should isolation of the work area with coffer dams also involve dewatering, hatchery personnel would electrofish the site to capture and relocate any listed species present within the coffered work zone

Throughout the year, gravel, sediment and small woody debris is deposited in the vicinity of the Satellite Facility diversion dams and water supply intake structures at both the upper and lower Crooked River and Red River and Powell sites. The accumulation of sediment and debris has the potential to restrict the volume of water that can be diverted to the hatchery. Materials must be removed annually to ensure an uninterrupted supply of water for fish culture and trapping operation. The diversion dams and water source intake structures may become damaged by the seasonal movement and deposition of sediment and large woody debris. These structures may Page 31

need to be temporarily removed for repair or replacement.

Removal of accumulated sediment or woody debris may be accomplished using a variety of techniques ranging from a clam shell type excavation bucket mounted to a crane, to a tracked or rubber tired excavator. In all cases, excavation equipment will not enter the stream channel. Access within the wetted perimeter of the stream will be limited to workers using hand tools, mud and sand suction dredges or guiding the operation of the heavy equipment. In some instances it may be desirable to construct small cofferdams using ecology blocks lined with heavy mil plastic sheeting to isolate the work area from the river channel.

The diversion dams and water source intakes are located within the migration and spawning habitat of ESA listed steelhead and Bull Trout. Direct effects to individual adult or juvenile Bull Trout and steelhead are a concern during all in-river maintenance activities. Effects could include disturbance and displacement of fish as a result of personnel or heavy equipment working near the river channel. A small sediment plume will likely be created as a result of substrate disturbance. This plume will persist for a short distance downstream and could affect embryonic life stages of Chinook salmon and steelhead or Bull Trout. To minimize impacts to incubating Chinook salmon, steelhead or Bull Trout, all work will be completed within a work window of July 1 (post-steelhead fry emergence) to August 15 (pre-Chinook salmon spawning) previously established by NOAA Fisheries for similar construction projects within the vicinity of Satellite Facilities. All excavated material will be removed from the river and loaded into a truck for offsite disposal or spread evenly along the river bank or used as local dirt parking lot fill.

Adult fish weir: Following periods of high flow, sand and gravel accumulates in front of the adult fish weir and entrance to the fish ladder and trap used for capturing adult spring and summer Chinook salmon and steelhead returning to the hatchery. This gravel accumulation restricts river flow and may encourage bank erosion, resulting in further sedimentation or damage to hatchery structures and equipment.

Removal of accumulated sediment or woody debris may be accomplished using a variety of techniques ranging from a clamshell type excavation bucket mounted to a crane, to a tracked or rubber tired excavator or workers operating mud and sand suction dredges. In all cases, excavation equipment will not enter the stream channel suction dredges will be mounted on floating devices. Access within the wetted perimeter of the stream will be limited to workers guiding the operation of the crane or excavator or workers operating mud and sand suction dredges. Excavated material will be loaded into a truck and hauled off site for disposal or spread evenly along the river bank or used as local dirt parking lot fill.. A small, short duration, sediment plume is anticipated during the excavation process. The adult fish trap and fish ladder is located within the migration corridor of spring Chinook salmon, steelhead and bull trout.

Aside from damages or loss of functionality related to high water events, the integrity of the adult weir may be compromised simply by age and exposure to changing weather conditions. Hatchery personnel must periodically complete a visual inspection of the structures by entering the river channel with hip boots, waders or dry suits with supplied air systems. Minor repairs may be completed in place by workers using hand tools, while more extensive repairs may require individual weir panels to be temporarily removed for repair or replacement. Should removal of these structures exceed the lifting capability of hatchery personnel, a crane or similar device operated from the stream bank would be employed. Heavy equipment will not enter the Page 32

stream channel. In some instances it may be necessary to construct a small cofferdam to isolate the work area from the river to facilitate repair work. Cofferdams would be constructed from sheet piling or ecology blocks lined with heavy mil plastic sheeting, thereby reducing the potential for sediment to escape and be transported downstream. Should isolation of the work area with coffer dams also involve dewatering, hatchery personnel would electrofish the site to capture and relocate any listed species present within the coffered work zone

Direct effects to individual adult or juvenile spring or summer Chinook salmon, steelhead and bull trout are a concern during these maintenance activities. Effects could include disturbance and displacement of fish as a result of personnel or heavy equipment working near the river channel. To minimize potential impacts to embryonic life stages of Chinook salmon or steelhead, all work will be completed within a work window of July 1 (post steelhead fry emergence) to August 15 (pre Chinook salmon spawning) previously established by NOAA Fisheries for similar construction projects within the vicinity. No machinery is placed in the river channel thus eliminating any risk of fuel or oil contamination. The removal of materials as described herein may occur as frequently as once each year depending upon the magnitude of spring runoff.

River bank stabilization: While infrequent, extreme high runoff events have the potential to erode the stream bank in the vicinity of the satellite facilities, causing localized flooding, damage to hatchery buildings or the interruption of water supplied to the facilities. To respond to threats of this nature it may be necessary to place fill material or rip rap within the river channel to control bank erosion. All materials used in such efforts would be clean (washed) rock to limit the introduction of sediment to the river channel. Machinery used for rock placement would be operated from outside the wetted perimeter of the stream to avoid the possibility of fuel or oil entering the water. Direct effects to individual adult or juvenile spring Chinook salmon, steelhead and bull trout are a concern during these maintenance activities. Effects could include disturbance and displacement of fish as a result of personnel or heavy equipment working near the river channel. At certain times of year impacts to embryonic life stages resulting from stream bank stabilization activities are also a concern; however, considering that such stabilizations activities would likely be done in response to extreme high river flows and localized flooding, the turbidity generated from the action would likely be less than what is already present in the river.

Programmatic Maintenance at the main Clearwater Fish Hatchery

The Clearwater Fish Hatchery receives water through two supply pipelines from Dworshak Reservoir. The warm water or surface intake is attached to a floating platform and can be adjusted from five feet to forty feet below the surface. The cool water intake is stationary at 245 feet below the top of the dam. When water temperatures drop in the fall, the surface intake is moved to the warmest water available until water temperatures rise in the spring. All water is gravity fed to the hatchery. The intake screens are in compliance with NMFS screen criteria by design of the Army Corp of Engineers. Floating debris and algae plug the intake screens and throughout the year small woody debris is deposited in the vicinity of the water supply intake structures at both the upper and lower level intake screens. The accumulation of debris has the potential to restrict the volume of water that can be diverted to the hatchery. Materials must be removed from the surface screen annually and the deep water screen intermittently to ensure an uninterrupted supply of water for fish culture operation.

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Removal of accumulated woody debris and algae and inspections of screens and piping may only be accomplished using a dive contractor certified and approved through Army Corps of Engineers security clearance protocol. Annually water supply intakes and supply pipelines will be temporarily shut down and emergency closure valves will be exercised inside the dam and at the hydropower plant. Both pipelines cross under the riverbed of the North Fork of the Clearwater River just upstream of the state Highway 7 bridge en route to the main hatchery. In the occasion of a pipeline maintenance event a coffer dam would be built parallel to the buried pipelines to accommodate heavy equipment to excavate and expose the pipeline construction/maintenance in accordance with Corps of Engineers guidelines as used with original construction.

Provide information regarding past takes associated with the hatchery program, (if known) including numbers taken, and observed injury or mortality levels for listed fish. No take of ESA-listed salmon or steelhead has been documented or is anticipated.

Provide projected annual take levels for listed fish by life stage (juvenile and adult) quantified (to the extent feasible) by the type of take resulting from the hatchery program (e.g. capture, handling, tagging, injury, or lethal take). No take from hatchery operations (adult trapping and broodstock collection) is anticipated. Estimated take by activity for hatchery programmatic maintenance and research/monitoring are provided in Appendix A; Tables 1a and 1b respectively. Take for juvenile trapping is covered under an annually renewed 4d Research permit for the Idaho Chinook Supplementation Study (2010- 14706).

Indicate contingency plans for addressing situations where take levels within a given year have exceeded, or are projected to exceed, take levels described in this plan for the program. We have not experienced any significant mortality of ESA-listed adult steelhead in conjunction with our maintenance activities at the satellite facilities. However, in the unlikely event that unforeseen conditions cause mortality of ESA-listed steelhead adults, maintenance activities will be immediately altered to eliminate the cause of the mortality. If necessary, activities will be suspended until corrections are completed.

SECTION 3. RELATIONSHIP OF PROGRAM TO OTHER MANAGEMENT OBJECTIVES

3.1 DESCRIBE ALIGNMENT OF THE HATCHERY PROGRAM WITH ANY ESU-WIDE HATCHERY PLAN OR OTHER REGIONALLY ACCEPTED POLICIES. EXPLAIN ANY PROPOSED DEVIATIONS FROM THE PLAN OR POLICIES This program conforms with the plans and policies of the Lower Snake River Compensation Plan administered by the U.S. Fish and Wildlife Service to mitigate for the loss of spring Chinook salmon production caused by the construction and operation of the four dams on the lower Snake River.

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The IDFG participated in the development of the Artificial Production Review and Evaluation (APRE) and Hatchery Scientific Review Group (HSRG) documents and is familiar with concepts and principals contained therein. This program is largely consistent with recommendations from these documents

3.2 LIST ALL EXISTING COOPERATIVE AGREEMENTS, MEMORANDA OF UNDERSTANDING, MEMORANDA OF AGREEMENT, OR OTHER MANAGEMENT PLANS OR COURT ORDERS UNDER WHICH PROGRAM OPERATES

2008-2017 Management Agreement for Upriver Spring Chinook, Summer Chinook and Sockeye pursuant to United States of America v. State of Oregon, U.S. District Court, District of Oregon.

Cooperative Agreement between the U.S. Fish and Wildlife Service and the Idaho Department of Fish and Game, FWS Agreement Nos.: 141102J010 - LSRCP Evaluation and Monitoring, 141102J009 - LSRCP Hatchery Operation

3.3 RELATIONSHIP TO HARVEST OBJECTIVES

The Lower Snake River Compensation Plan defined replacement of adults “in place” and “in kind” for appropriate state management purposes. Juvenile production and adult escapement targets were established at the outset of the LSRCP. The Hells Canyon Settlement Agreement defined mitigation goals in terms of smolts released. State and Tribal co-managers have established near and long term expectations for adult returns to Idaho Power facilities based on the smolt to adult return rates used to size the production capacity of the LSRCP hatcheries. State, tribal and federal co-managers work co-operatively to develop annual production and mark plans that are consistent with original LSRCP and Hells Canyon Settlement Agreement, the US vs. OR Management Agreement, and recommendations of the HSRG and HRT relative to ESA impact constraints, genetics, fish health and fish culture concerns.

In the Snake River basin, mitigation hatchery returns are harvested in both mainstem and tributary terminal fisheries. Fish that return in excess to broodstock needs for the hatchery programs are shared equally between sport and Tribal fisheries. State and Tribal co-managers cooperatively manage fisheries to maximize harvest of hatchery returns that are in excess of broodstock needs. Fisheries are managed temporally and spatially to: minimize impacts to non- target natural returns and comply with ESA incidental take limits; achieve hatchery broodstock goals; achieve sharing objectives among Tribal and recreational fisheries; optimize the quantity and quality of fish harvested that are in excess of what is needed to meet broodstock needs; maximize temporal and spatial extent of fishing opportunities; and minimize conflicts between different gear types and user groups

State and Tribal co-managers confer pre-season relative to assessing forecasted levels of abundance of both hatchery and natural fish in the fisheries. Forecasts are used to project likely non-tribal and tribal harvest shares. Incidental take rates applicable to fisheries are projected

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based on forecasted natural populations addressed in the 2000 Biological Opinion. As part of the in-season harvest management and monitoring program, the IDFG and Tribal cooperators conduct annual angler surveys to assess the contribution program fish make toward meeting program harvest mitigation objectives. The surveys are also used for in-season assessments of recreational and Tribal harvest shares and to determine ESA take relative to allowable levels based on the sliding scales of natural spawner abundance. In-season, state, tribal, and federal co- managers conduct weekly teleconferences in concert with web-based data sharing tools to confer about harvest and incidental take levels and the disposition of fish captured at the hatchery traps in excess of broodstock needs. Co-managers also conduct meetings after fisheries conclude to assess the success of the management actions taken during the season. 3.3.1 Describe fisheries benefiting from the program, and indicate harvest levels and rates for program-origin fish for the last twelve years, if available.

The Clearwater River Basin salmon fishery targets hatchery fish produced by Dworshak National Fish Hatchery, Kooskia National Fish Hatchery, Nez Perce Tribal Hatchery, and the Clearwater Fish Hatchery and its satellites. When fishing seasons are held, the following areas are typically open: 1) mainstem Clearwater River, 2) North Fork Clearwater River, 3) South Fork Clearwater River, and 4) Lochsa River.

Harvest data for 1997-2007 is displayed in Table 17 below. These estimates do not include harvest downstream of Idaho.

Table 17. Estimated number of Chinook harvested in Clearwater Basin 1997- 2007. Harvest Year Estimated Chinook Estimated Harvest Harvest in from Clearwater Clearwater Basin Hatchery Releases 1997 738 No Estimate 1998 99 No Estimate 1999 No Season No Season 2000 4,384 316 2001 21,883 7,131 2002 6,986 1,899 2003 3,010 356 2004 7,704 1,901 2005 1,085 420 2006 793 131 2007 724

3.4 RELATIONSHIP TO HABITAT PROTECTION AND RECOVERY STRATEGIES

Hatchery production for harvest mitigation is influenced but not specifically linked to habitat protection strategies in the Clearwater basin and other areas. The NMFS has not developed a

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recovery plan specific to Snake River Chinook salmon, but the Clearwater program is operated consistent with existing Biological Opinions.

3.5 ECOLOGICAL INTERACTIONS

The possibility of collecting ESA-listed salmon or steelhead during broodstock collection in upper Clearwater River tributaries is remote. Fall Chinook and sockeye salmon adults are temporally and spatially separated from broodstock collection at the Clearwater Fish Hatchery satellite weirs. Several studies have shown Chinook to have a high degree of fidelity to natal stream or release site (Bowles and Leitzinger 1991). The satellite weirs are over 100 miles from the mouth of the Clearwater River. We cannot differentiate spring Chinook naturally produced in the upper Clearwater drainage from listed spring/summer Chinook. We have no indication that marked hatchery fish from even the same geographic area as listed Chinook salmon (such as McCall summer Chinook) are being collected in the upper Clearwater River. We conclude there would is no effect to listed salmon from our adult spring Chinook broodstock collection at the Clearwater Fish Hatchery satellite weirs.

In addition to broodstock collection, adults may be out-planted from a satellite weir site to spawning areas upstream for research or supplementation. Adult out-plants will not exceed estimated carrying capacity of rearing habitat for their progeny, so we conclude there would be no effect to listed salmon from this action.

The LSRCP "Hatchery Evaluation Study Program" in the Clearwater River will continue studies initiated to determine hatchery rearing and release strategies that will help meet the mitigation requirements of the LSRCP program and the management goals of the IDFG. Within this goal, the hatchery program will attempt to improve the survival of hatchery fish while avoiding negative effects to natural populations. Two primary objectives are central to achieving this goal: 1) evaluate the success of the LSRCP program in meeting specified goals and 2) identify factors limiting hatchery success and recommend possible improvements based on existing knowledge and experimentation. Hatchery operation studies have focused on the monitoring and evaluation of hatchery loading and size variables, timing of release studies, location of release studies, and natural rearing studies.

Angler surveys will continue to assess the LSRCP contribution to Idaho's steelhead and Chinook fisheries, estimate the total escapement of LSRCP fish, recover information on marked fish, and obtain data for managing fisheries while protecting wild stocks. We do not believe that any of these ongoing studies adversely affect listed salmon or steelhead species.

The physical operation of the Clearwater Fish Hatchery and its satellites is expected to have no affect on listed salmon or steelhead. All effluents must meet existing water quality standards. Water sources are properly screened and maintained so as to not affect listed salmon or steelhead.

Hatchery spring Chinook salmon from the Clearwater Fish Hatchery program enter the Snake River emigration corridor at Lower Granite Reservoir. Their presence in the reservoir overlaps to some degree with listed sockeye, spring/summer Chinook salmon, and steelhead. We believe Chinook from the program are temporally separated from listed fall Chinook salmon in the reservoir based on different migration periods.

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Our current hatchery practices include measures to control pathogens. Bacterial Kidney Disease (BKD) continues to persist in hatcheries, but it is also endemic in naturally spawning populations. Efforts to minimize BKD incidence in hatcheries, such as adult disease testing, culling, and single family incubation, will continue. There is no evidence that horizontal transmission of disease from the Clearwater Fish Hatchery program to listed species occurs or has a measurable effect on listed species survival and recovery.

We conclude that the LSRCP spring Chinook program in the upper Clearwater River is not likely to jeopardize the continued existence or the recovery of listed spring/summer Chinook salmon, sockeye salmon, fall Chinook salmon or steelhead.

There is no effect from the Clearwater Fish Hatchery program to listed spring/summer Chinook salmon in their production area. We believe that even with low abundance of listed Chinook salmon, the potential of affecting them with the Clearwater Fish Hatchery program by straying of adults, disease transmission, or competitive effects in the migration corridor, is remote.

Fall Chinook salmon are temporally and spatially separated from the LSRCP spring Chinook salmon release and should not be adversely affected.

Sockeye are spatially separated from the LSRCP spring Chinook salmon release until they enter Lower Granite Reservoir. It appears that there is also some temporal separation of migration timing. Most of the hatchery fish have probably passed through Lower Granite Reservoir by the time sockeye arrive, in years of normal water conditions.

SECTION 4. WATER SOURCE

4.1 PROVIDE A QUANTITATIVE AND NARRATIVE DESCRIPTION OF THE WATER SOURCE (SPRING, WELL, SURFACE), WATER QUALITY PROFILE, AND NATURAL LIMITATIONS TO PRODUCTION ATTRIBUTABLE TO THE WATER SOURCE

Clearwater Fish Hatchery - The Clearwater Fish Hatchery receives water through two supply pipelines from Dworshak Reservoir. The warm water intake is attached to a floating platform and can be adjusted from five feet to forty feet below the surface. The cool water intake is stationary at 245 feet below the top of the dam. An estimated 10 cfs is provided by the cool water supply and 70 cfs is provided from the warm water supply. The cool water supply has remained fairly constant between 38°F and 45°F. The warm water can reach 80°F but is adjusted regularly to maintain 56°F for as long as possible throughout the year. When water temperatures drop in the fall, the intake is moved to the warmest water available until water temperatures rise in the spring. All water is gravity fed to the hatchery. The intake screens are in compliance with NMFS screen criteria by design of the Army Corp of Engineers.

Red River Satellite - Red River’s water source is from the South Fork of Red River where a

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hand built diversion diverts water into a screen on the bottom of the river and a pipeline delivers it to the rearing pond and adult facility. The intake screens are in compliance with NMFS screen criteria by design of the Army Corp of Engineers.

Crooked River Satellite - Crooked River’s water source is from Crooked River where a concrete weir with dam board slot is used to control water level at the facility. The intake screens are in compliance with NMFS screen criteria by design of the Army Corp of Engineers.

Powell Satellite – The water source is from Walton Creek where a concrete weir structure with sheet pilings and vertical screens diverts water to the rearing pond and adult facility. The intake screens are in compliance with NMFS screen criteria by design of the Army Corp of Engineers.

4.2 INDICATE RISK AVERSION MEASURES THAT WILL BE APPLIED TO MINIMIZE THE LIKELIHOOD FOR THE TAKE OF LISTED NATURAL FISH AS A RESULT OF HATCHERY WATER WITHDRAWAL, SCREENING, OR EFFLUENT DISCHARGE

The intake screens comply with NMFS screen criteria and were designed by the Army Corp of Engineers.

SECTION 5. FACILITIES

5.1 BROODSTOCK COLLECTION FACILITIES (OR METHODS)

The main Clearwater Hatchery is not a collection facility, but it does have an adult holding facility. This consists of two ponds with a combined capacity of 8,000 cubic feet and a maximum holding capacity of 1,000 adult salmon. Each pond measures 10 feet x 100 feet with an average depth of four feet. There is a covered spawning area with live tanks at the head of each holding pond.

Clearwater Fish Hatchery satellite facilities are described in Section 5.3 below.

5.2 FISH TRANSPORTATION EQUIPMENT (DESCRIPTION OF PEN, TANK TRUCK, OR CONTAINER USED)

The following transportation equipment is available for use by the Clearwater Fish Hatchery:

10 wheel smolt transport truck fitted with three 850 gallon compartments supplied with oxygen and fresh flow agitator systems

10 wheel adult transport truck fitted with two 1,000 gallon compartments supplied with oxygen and fresh flow agitator systems

2-ton transport truck fitted with two 500 gallon compartments supplied with oxygen and fresh flow agitator systems

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1-ton transport truck fitted with one 300 gallon compartment supplied with oxygen and fresh flow agitator systems

100 gallon transfer tank supplied with oxygen. This container is transported by forklift and is used for moving fish from one location to another on the hatchery grounds.

5.3 BROODSTOCK HOLDING AND SPAWNING FACILITIES

Clearwater Hatchery - The main Clearwater Hatchery is not a collection facility, but it does have an adult holding capability. This consists of two ponds with a combined capacity of 8,000 cubic feet and a maximum holding capacity of 1,000 adults. Each pond measures 10 x 100 feet and has an average depth of four feet. There is a covered spawning area with live tanks at the head of each holding pond.

Red River - The Red River Satellite facility has an adult trapping and holding facility. The two adult holding ponds measure 10 x 45 feet with an average depth of 4 feet. Total holding space is 3,600 cubic feet with a total holding capacity of 400 adult fish, and is supplied with 4.09 cfs of water. This facility also has a covered spawning area with live tanks at the head of each holding pond.

Crooked River – The Crooked River facility has no broodstock holding or spawning capability.

Powell - The Powell facility also has two adult ponds measuring each 100 foot x 10 ft x 4 feet 8 inches. The volume of the two ponds is 9,500 cubic feet with a long-term holding capacity of 1,000 adult Chinook and a short-term capacity of 1,200. It is supplied with 6.24 cfs of water. There is a covered spawning area with live tanks at the head of each holding pond.

5.4 INCUBATION FACILITIES

The Clearwater Hatchery incubation room contains 49 double-stack Heath incubators with a total of 784 trays available for egg incubation. The upper and lower halves of each stack (eight trays each) have a different water supply and drain. This design aids in segregation of diseased eggs. The maximum capacity of this facility is five million green eggs. The incubation room is supplied with both reservoir water sources to provide the desired temperature for incubation at a flow of 5 to 8 gallons per minute (gpm) per one-half stack.

Isolation incubation consists of 16 double-stack Heath incubators with a total of 256 trays available for egg incubation. The maximum capacity of this facility is 1.5 million green eggs. The isolation incubation room is supplied with both reservoir water sources to provide the desired temperature for incubation with a flow of 5 to 8 gpm per stack.

5.5 REARING FACILITIES

Clearwater Fish Hatchery - Chinook salmon raceways are 200 feet x 10 feet x 3 feet deep. Eleven raceways have a total rearing space of 66,000 cubic feet. The raceways are supplied with water from both primary and secondary intakes and a mixing chamber, which allows for the control of water temperature. The designed rearing capacity of these raceways is 1.5 million smolts at a 0.3 density index (DI). The estimated flow per raceway is 2.4 cfs. Additional rearing

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space is available in the steelhead raceway structure.

Early rearing space consists of 60 concrete vats. Each vat measures 40 feet x 4 feet x 3 feet deep and contain 480 cubic feet of rearing space. This part of the facility can rear 5.9 million fish to 287 fish/lb. at a 0.3 DI. The vats are supplied with water from each reservoir intake and have a flow of approximately 120 gpm per vat when all vats are in use. An incubation jar is plumbed directly into each vat. The 60 incubator jars have a total capacity of 2.6 million eggs with a flow of 15 gpm per jar.

Crooked River - The Crooked River facility has two raceways, measuring 145 feet x 20 feet x 4 feet deep, for a total of 23,200 cubic feet. These raceways have a capacity of 700,000 juveniles at a DI of 0.29. Water flow per raceway is 6 cfs. Each raceway is outfitted with three automated Nielson feeders.

Red River – The Red River facility has one 170 foot x 70 foot x 4 foot-6 in. deep rearing pond with a maximum capacity of 320,000 juveniles at a DI of less than 0.3 and a maximum capacity of 500,000 smolts at a DI of 0.092. Maximum water flow through this pond is 6.24 cfs. This pond has a hypalon plastic liner with cobblestones placed on the inclined banks to hold the liner in place. The bottom of the pond is bare, which aids in pond vacuuming. A catwalk runs the entire length of the rearing pond and holds eight automated Nielson feeders. .

Powell - The rearing pond measures 165 feet x 65 feet x 5 feet deep and has 53,625 cubic feet of rearing space. The normal loading rate of 320,000 fish equates to a DI significantly less than 0.3. The maximum design capacity is 500,000 fish with a DI of 0.092. Water flow through this pond is 6.24 cfs. A catwalk across the length of the pond supports eight automated Nielson feeders.

5.6 ACCLIMATION/RELEASE FACILITIES

Same as described in Section 5.5 above.

5.7 DESCRIBE OPERATIONAL DIFFICULTIES OR DISASTERS THAT LED TO SIGNIFICANT FISH MORTALITY

Infrequent but significant fish mortality has occurred at the Crooked River and Powell satellites when water intake systems become obstructed with debris and slush ice during periods of high water discharge and low air temperatures during spring acclimation.

5.8 INDICATE AVAILABLE BACK-UP SYSTEMS AND RISK AVERSION MEASURES THAT WILL BE APPLIED THAT MINIMIZE THE LIKELIHOOD FOR THE TAKE OF LISTED NATURAL FISH THAT MAY RESULT FROM EQUIPMENT FAILURE, WATER LOSS, FLOODING, DISEASE TRANSMISSION, OR OTHER EVENTS THAT COULD LEAD TO INJURY OR MORTALITY.

Clearwater Fish Hatchery - An alarm system monitors for low water in each rearing area and

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high water temperature on the warm water supply. Hatchery staff checks raceway flows and temperatures manually on a daily schedule.

Red River – A low water alarm system is installed in the adult holding and acclimation/rearing ponds. A rigorous screen cleaning schedule has been implemented to insure that screens stay clear of debris during periods of high discharge.

Crooked River - A low water alarm system is installed in the juvenile rearing raceway. Living quarters have recently been built on station to house staff. Staff monitors intake screens day and night during spring acclimation. When nightly air temperatures drop to 29˚C, screens are cleaned as often as necessary to maintain constant flow of water to raceway.

Powell – An alarm system is in place to detect low water resulting from an obstructed water intake. A rigorous screen cleaning schedule has been implemented to insure that screens stay clear of debris during periods of high discharge. When nightly air temperatures drop below 29˚C, screens are cleaned as often as necessary to maintain constant flow of water to the rearing pond.

SECTION 6. BROODSTOCK ORIGIN AND IDENTITY

This section describes the origin and identity of broodstock used in the program, its ESA-listing status, annual collection goals, and relationship to wild fish of the same species/population.

6.1 SOURCE

Founding hatchery stocks used for spring Chinook salmon reintroductions were primarily obtained from the Rapid River Hatchery (Kiefer et al. 1992; Nez Perce Tribe and Idaho Department of Fish and Game 1990). Initially however, spring Chinook stocks imported for restoration came from Carson, Big White, Little White or other spring Chinook captured at Bonneville Dam (Nez Perce Tribe and Idaho Department of Fish and Game 1990). Genetic analyses confirm that existing natural spring Chinook salmon in the Clearwater River subbasin are derived from reintroduced Snake River stocks (Matthews and Waples 1991).

6.2 SUPPORTING INFORMATION

6.2.1 History

Red River – The Red River pond was built in 1977 under the Columbia River Fisheries Development Project and was administered by NMFS, IDFG, USFS, and the Pacific Northwest Regional Commission until 1986. In 1986, a permanent adult trapping facility and holding complex was constructed by the Army Corps of Engineers as part of the LSRCP. Between 1977 and 1980 and in 1983 and 1987, and between 1990 and 1994, Rapid River stock spring Chinook fingerlings were released at the Red River satellite (Bowles and Leitzinger 1991). Carson National Fish Hatchery fingerlings were released in 1981. From 1982 through 1985, only adults returning to the Red River satellite were used to source eggs for broodstocks. However, Dworshak National Fish Hatchery supplied juveniles for the 1988 release when Red River fish had to be destroyed due to the presence of Infectious Pancreatic Necrosis Virus (IPN). In 1987

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and from 1989 through 1992, Red River stock smolts reared at Kooskia and Dworshak National Fish hatcheries were released at the Red River facility. Since 1997, Red River and Crooked River stocks have generally been treated as one stock with respect to broodstock management.

Crooked River – The Crooked River satellite has been in operation as part of the LSRCP since 1990. Juvenile Chinook salmon produced at Rapid River Hatchery and at Dworshak National Fish Hatchery were released at this location in 1989. Juvenile Chinook salmon were released from Kooskia National Fish Hatchery in 1990 and 1991 (Bowles and Leitzinger 1991). Eyed- eggs received in 1994 from Rapid River/Looking Glass hatchery stock were also incorporated into the program. In 1995, all fish released at the Crooked River facility originated from Rapid River stock. In 1996 and 1998, only Crooked River adults were used to develop broodstocks. Since 1997, Red River and Crooked River stocks have been treated as one stock with respect to broodstock management.

Powell – The founding broodstock for the Powell satellite was sourced from the Lochsa River at the confluence of Colt Killed Creek and Crooked Fork Creek. Kooskia and Dworshak National Fish hatcheries provided juveniles for release between 1989 and 1991. In 1999, juveniles produced from Rapid River stock were released from the Powell satellite.

6.2.2 Annual size

No ESA-listed spring Chinook salmon are trapped as part of this program and no natural-origin Chinook salmon are used for broodstock. Annual guidelines for broodstock size are listed below. As the Nez Perce Tribal Hatchery comes on line in the near future, production associated with this program that is currently being accommodated by the Clearwater Fish Hatchery will become a tribal responsibility at their new facility.

The current spring/summer Chinook salmon program at the Clearwater Hatchery includes the release of 2,635,000 spring-run Chinook salmon and 200,000 summer-run Chinook salmon. Managers intend to increase the summer run component over time to one million yearling smolts. To achieve the current release goals, approximately 980 spring-run and 60 summer-run females are collected for broodstock along with a similar number of males to achieve a 1:1 spawn ratio. Additionally, IDFG provides eggs up to 200 females to the Nez Perce Tribe for programs operated out of the Nez Perce Tribal Hatchery.

South Fork Clearwater River Program – Red River and Crooked River traps (IDFG mitigation program):

Approximate adult spawn target: 500 females (approximately 2.026 million green eggs)

South Fork Clearwater River Program – Red River and Crooked River traps (Nez Perce Tribal supplementation program):

The NPT requests eggs from up to 200 females

Lochsa River Program – Powell trap (IDFG mitigation program):

Approximate adult spawn target: 483 females (approximately 1.94 million eggs)

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6.2.3 Past and proposed level of natural fish in broodstock

See Section 6.2.1 above. No ESA-listed or endemic fish were used to source the Clearwater Fish Hatchery spring Chinook salmon program. Natural stocks were extirpated by Lewiston Dam.

6.2.4 Genetic or ecological differences

The Clearwater Fish Hatchery spring Chinook salmon program will have no genetic or ecological effect on endemic stocks. Genetic analyses confirm that existing natural spring Chinook salmon in the Clearwater River subbasin are derived from reintroduced Snake River stocks (Matthews and Waples 1991).

Genetic analyses using 13 microsatellite loci have indicated that Snake River Chinook salmon exhibit structuring within subbasins (including the Clearwater), meaning the populations within a subbasin are genetically differentiated as a result of strong philopatry (Narum et al. 2007). However, populations within a subbasin generally cluster together, independent from other subbasins (Narum et al. 2007). The exceptions involve wild and hatchery stock comparisons. For example, Narum et al. (2007) observed that all of the stream-type collections from the Clearwater River (hatchery and wild) cluster tightly with samples from the Rapid River Hatchery, and the collections of natural ocean types from the Clearwater River (three temporal replicates combined) were not significantly different from either Lyons Ferry Hatchery or the Nez Perce Tribal Hatchery. Populations in subbasins that have not received large numbers of out of basin hatchery stocking (e.g. M.F. Salmon River, S.F. Salmon River) appear genetically distinct and do not cluster with hatchery stocks. Narum et al. (2007) found no evidence that re- established Chinook salmon populations in the Clearwater River subbasin were genetically bottlenecked, nor that they exhibit any unique remnant genetic variation.

6.2.5 Reasons for choosing

Endemic spring Chinook salmon stocks in the Clearwater River basin were extirpated by Lewiston Dam (1927 to 1972). As such, an endemic broodstock could not be used to found this program.

6.3 INDICATE RISK AVERSION MEASURES THAT WILL BE APPLIED TO MINIMIZE THE LIKELIHOOD FOR ADVERSE GENETIC OR ECOLOGICAL EFFECTS TO LISTED NATURAL FISH THAT MAY OCCUR AS A RESULT OF BROODSTOCK SELECTION PRACTICES.

No adverse impacts or effects to the listed population are expected as wild/natural adults are not currently trapped and used for broodstock purposes.

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SECTION 7. BROODSTOCK COLLECTION

7.1 LIFE-HISTORY STAGE TO BE COLLECTED (ADULTS, EGGS, OR JUVENILES)

All broodstock collected for this program come from hatchery-origin adults.

7.2 COLLECTION OR SAMPLING DESIGN

At this time no unmarked (natural origin) fish are incorporated into the hatchery broodstock. All adult fish collected for broodstock at all locations are of hatchery origin. Fish are selected randomly from ripe fish during weekly spawning events.

Red River - Collection is accomplished by a weir across Red River, diverting fish into the trapping facility.

Crooked River - Collection is accomplished by a weir across Crooked River, diverting fish into the trapping facility.

Powell - The fish encounter no weir on the Lochsa River and turn into the attraction water of Walton Creek where they were acclimated and released as smolts.

7.3 IDENTITY

All harvest mitigation hatchery-produced fish are marked with an adipose fin clip. Releases for supplementation programs may be marked with a pelvic fin clip or CWT and no fin clip.

7.4 PROPOSED NUMBER TO BE COLLECTED

7.4.1 Program goal (assuming 1:1 sex ratio for adults)

No ESA-listed spring Chinook salmon are trapped as part of this program. Annual guidelines for broodstock size are listed below. The current spring/summer Chinook salmon program at the Clearwater Hatchery includes the release of 2,635,000 spring run Chinook salmon and 200,000 summer run Chinook salmon. To achieve these release goals, approximately 980 spring run and 60 summer run females are collected for broodstock along with a similar number of males to achieve a 1:1 spawn ratio. Additionally, IDFG provides eggs from up to 200 females to the Nez Perce Tribe for other programs operated in the Clearwater River drainage.

South Fork Clearwater River Program – Red River and Crooked River traps (IDFG mitigation program):8

Approximate adult spawn target: 500 females (approximately 2.026 million green eggs)

Nez Perce Tribal Hatchery (NPTH) program – Red River and Crooked River traps (Nez Perce Tribal supplementation program):

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The NPT requests eggs from up to 200 females for production at NPTH.

Lochsa River Program – Powell trap (IDFG mitigation program):

Approximate adult spawn target: 483 females (approximately 1.94 million eggs)

7.4.2 Broodstock collection levels for the last twelve years or for most recent years available

Information presented in Table 18 represents broodstock collection all satellite facilities.

Table 18. Composition of broodstock collected from 1994-2009.

Adults Brood Year Females Males/unknowns Jacks Eggs1 Juveniles2 1994 86 56 2 327,085 361,622 1995 2 7 15 19,270 200,062 1996 178 223 146 590,371 806,057 1997 1,011 913 8 2,676,981 3,210,461 1998 388 379 3 1,558,101 1,475,862 1999 41 39 264 929,353 781,823 2000 1,352 705/ 118 959 2,750,100 3,780,880 2001 2,476 1,795/ 1,328 91 4,577,790 3,686,681 2002 1,876 1,386/ 19 72 3,316,427 n/a 2003 1,022 832 175 2,789,194 1,980,046 2004 1,075 1,190 96 2,915,056 2,562,906 2005 221 214 76 780,764 1,670,006 2006 916 611 127 2,807,896 2,603,931 2007 861 638 617 2,542,933 2,577,686 2008 1,139 853 419 3,825,480 n/a 2009 917 629 556 3,387,415 n/a 1 Not all adults trapped are spawned. Adults may be released for natural spawning or recycled in the sport fishery. 2 Release numbers may include juveniles received as eyed-eggs from other facilities.

7.5 DISPOSITION OF HATCHERY-ORIGIN FISH COLLECTED IN SURPLUS OF BROODSTOCK NEEDS

Crooked River and Red River – In the past, hatchery-origin adults that were part of a supplementation experiment were passed above weirs to spawn naturally. Currently, only natural-origin returns are passed above the weirs. General production fish that return in excess of broodstock needs are recycled through the sport fishery or out-planted according to management agreements.

Powell – In the past, hatchery-origin adults that were part of a supplementation experiment were

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passed above weirs to spawn naturally. Currently, only natural-origin returns are passed above the weirs. General production fish that return in excess of broodstock needs are recycled through the sport fishery or are out-planted according to management agreements.

7.6 FISH TRANSPORTATION AND HOLDING METHODS

Adult spring Chinook salmon trapped at Crooked River are transported daily to the Red River satellite holding facility. All fish trapped at Red River and Crooked River are transferred to the main Clearwater Fish Hatchery for final holding and spawning. At the time of transfer, fish are measured, injected with Erythromycin (20 mg/kg), inspected for injuries, and scanned for CWT, PIT, and radio tags. Fish are transferred using adult transport vehicles.

Pre-spawn adults are held in adult holding facilities described above. Fish receive routine treatments with formalin (125 ppm) to control the spread of fungus.

7.7 DESCRIBE FISH HEALTH MAINTENANCE AND SANITATION PROCEDURES APPLIED

Fish receive routine treatments with formalin (125 ppm) to control the spread of fungus. At spawning, eggs from females exhibiting gross clinical signs of bacterial kidney disease may be culled. Tissue is sampled from each spawned female and analyzed for viral pathogens and for the causative agent responsible for bacterial kidney disease.

7.8 DISPOSITION OF CARCASSES

All pre-spawning mortality fish are disposed of in a sanitary landfill. Carcasses generated by spawning activities may be returned to upper tributaries for stream nutrient enhancement. All carcasses that exhibit gross clinical signs of bacterial kidney disease are disposed of in a landfill.

7.9 INDICATE RISK AVERSION MEASURES THAT WILL BE APPLIED TO MINIMIZE THE LIKELIHOOD FOR ADVERSE GENETIC OR ECOLOGICAL EFFECTS TO LISTED NATURAL FISH RESULTING FROM THE BROODSTOCK COLLECTION PROGRAM

Only hatchery-origin, non ESA-listed adults are collected for broodstock purposes.

SECTION 8. MATING

This section describes fish mating procedures that are used, including those applied to meet performance indicators identified previously.

8.1 SELECTION METHOD

Female spring Chinook salmon are sorted two times per week. Generally, two spawn days occur each week. Males are randomly selected for spawning on each spawning day.

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As each male is spawned, it receives an opercle punch and is placed back into the holding pond. Males are generally not used more than two times. Every effort is made to use all returning fish for spawning during the spawning year. At least five to ten percent of the males used for spawning will be composed of jacks.

8.2 MALES

See Section 8.1.

8.3 FERTILIZATION

Spawning ratios of 1 male to 1 female will be used when the broodstock population contains more than 100 females. If the spawning population contains between 50 and 100 females, then eggs from each female are split into two equal sub-families. Each sub-family is fertilized by a different male. One cup of well water is added to each bucket and set aside for 30 seconds to one minute. The two buckets are then combined.

When the broodstock population contains 50 to 26 females, the eggs from each female are split into three equal sub-families. Each sub-family is fertilized by a different male. One cup of well water is added to each bucket and set aside for 30 seconds to one minute. All three sub-families are then combined.

When the broodstock population contains 25 females or less, the eggs from each female are divided into four equal sub-families. Each sub-family is fertilized by a separate male. The process is completed as previously mentioned to finish the spawning process. An effort is made to use all returning fish for spawning.

8.4 CRYOPRESERVED GAMETES

Milt is not cryopreserved as part of this program, and no cryopreserved gametes are used in this program.

8.5 INDICATE RISK AVERSION MEASURES THAT WILL BE APPLIED TO MINIMIZE THE LIKELIHOOD FOR ADVERSE GENETIC OR ECOLOGICAL EFFECTS TO LISTED NATURAL FISH RESULTING FROM THE MATING SCHEME

No natural-occurring fish are incorporated into the spawning operation.

SECTION 9. INCUBATION AND REARING

This section specifies management goals (e.g., egg to smolt survival) that the hatchery is currently operating under for the hatchery stock. Data is provided on the success of meeting the desired hatchery goals.

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9.1 INCUBATION

9.1.1 Number of eggs taken and survival rates to eye-up and/or ponding

Table 19. Survival from green to eyed stage for eggs taken from 1988 through 2009 at Clearwater Fish Hatchery

Survival to Green Eggs Spawn Year Eyed-eggs Eyed Stage Taken (%) 1988 391,743 N/A N/A 1989 N/A N/A N/A 1990 24,000 N/A N/A 1991 24,200 16,051 66.3 1992 543,878 495,045 91.0 1993 1,651,269 1,382,719 83.7 1994 327,085 303,464 92.8 1995 9,635 7,130 74.0 1996 590,371 537,828 91.1 1997 2,759,300 2,457,191 89.1 1998 1,228,047 1,006,067 82.0 1999 907,614 855,384 94.2 2000 2,750,100 ¹ 2,379,681¹ 86.5 2001 3,551,769² 3,330,700² 93.8 2002 3,028,970² 2,906,538² 96.0 2003 2,375,481³ 2,186,760³ 92.1 2004 2,915,056 2,739,433 94.0 2005 780,764 1,3 747,174 1,3 95.7 2006 2,807,896 2,689,849 95.8 2007 2,515,447 2,361,027 93.9 2008 3,825,480 3,574,039 93.4 2009 3,387,415¹ 3,176,606 93.7 ¹Does not include eggs transferred from Rapid River ²Does not include eggs collected for Nez Perce Tribal programs ³Does not include eggs collected from Dworshak

9.1.2 Cause for, and disposition of surplus egg takes

Surplus eggs may be generated (~ 10% above need) to provide a buffer against culling associated with the presence of bacterial kidney disease.

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9.1.3 Loading densities applied during incubation

Fertilized Chinook salmon eggs are loaded in Heath trays at densities that do not exceed 8,000 eggs per tray.

9.1.4 Incubation conditions

The maximum isolation incubation capacity of this facility is 6.272 million green eggs. The incubation room is supplied with two water sources to provide the desired temperature for incubation with a flow of 5 to 8 gpm per one-half stack.

Isolation incubation consists of 16 double stack Heath incubators with a total of 256 trays available for egg incubation. The maximum capacity of this facility is 2.048 million green eggs. The isolation incubation room is supplied with both water sources to provide the desired temperature for incubation with a flow of 5 to 8 gpm per stack.

Eyed-eggs are typically loaded in Heath tray baskets at densities not to exceed 8,000 eggs per basket.

Water flow to each incubator stack is checked periodically to insure that desired flows are maintained. Incubator water temperatures are tracked with recording thermographs and hand- held thermometers.

9.1.5 Ponding

Fry are typically ponded in hatchery vats when 80% of each incubation tray has completed yolk absorption. Temperature units are tracked throughout incubation to assist with the process of tracking incubation development. Spring Chinook salmon are typically ponded from December through the end of January. Flow and density indices are maintained to not exceed 1.3 and 0.3, respectively (Piper et al. 1982).

9.1.6 Fish health maintenance and monitoring

Following fertilization, eggs are typically water-hardened in a 100 ppm Iodophor solution for 30 minutes. During incubation, eggs routinely receive scheduled formalin treatments to control the growth of fungus. Treatments are typically administered three times per week at a concentration of 1667 ppm active ingredient. Formalin treatments are discontinued prior to hatching. Prior to hatching, dead eggs are picked on a regular schedule (approximately two times per week) to discourage the spread of fungus.

9.1.7 Indicate risk aversion measures that will be applied to minimize the likelihood for adverse genetic and ecological effects to listed fish during incubation

No adverse genetic or ecological effects to listed fish are anticipated as only hatchery-origin adults are spawned.

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9.2 REARING

9.2.1 Provide survival rate data (average program performance) by hatchery life stage (fry to fingerling; fingerling to smolt) for the most recent twelve years or for years dependable data are available

Table 20. Brood year percent survival by life stage from 1997-2008. Brood Year Fry to fingerling Fingerling to smolt percent survival percent survival 1997 97.7 96.0 1998 99.7 99.9 1999 89.8 99.5 2000 99.3 99.3 2001 92.0 91.4 2002 99.2 99.4 2003 99.2 99.7 2004 99.4 99.2 2005 99.3 99.8 2006 97.8 92.8 2007 99.0 99.4 2008 99.9 N/A

9.2.2 Density and loading criteria (goals and actual levels)

At the swim-up stage of development, unfed fry are moved to inside vats and distributed as evenly as possible (typically 15,000 to 44,000 fish per vat at ponding). Density (DI) and flow (FI) indices are maintained to not exceed 0.30 and 1.3, respectively (Piper et al. 1982).

9.2.3 Fish rearing conditions

Clearwater Fish Hatchery - Chinook raceways are 200 feet x 10 feet x 3 feet deep. Eleven raceways have a total rearing space of 66,000 cubic feet. The raceways are supplied with water from both primary and secondary intakes and a mixing chamber, which allows water temperature to be controlled to rear Chinook. The designed rearing capacity of these raceways is 1.5 million smolts at a 0.3 DI. The estimated flow per raceway is 2.4 cfs.

Early rearing space consists of sixty concrete vats. Each measures 40 feet x 4 feet x 3 feet deep and contains 480 cubic feet of rearing space. This part of the facility can rear 5.9 million fish to a size of 287 fish/lb. at a 0.3 DI. The vats are supplied with water from each intake and have a flow of approximately 120 gallons per minute per vat when all vats are in use. An incubation jar is plumbed directly into each vat. The 60 incubator jars have a total capacity of 2.6 million eggs with a flow of 15 gpm per jar.

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Crooked River - The Crooked River facility has two raceways, measuring 145 feet x 20 feet x 4 feet deep, for a total of 23,200 cubic feet. These raceways have a capacity of 700,000 juvenile Chinook with a DI of 0.29. Water flow per raceway is 6 cfs. Each raceway is outfitted with three automated Nielson feeders. The adult trapping facility measures 10 feet x 12 feet x 4 feet deep with a total of 480 cubic feet. Water flow for the adult facility is 10 cfs. This facility has no provision for adult holding.

Powell - The rearing pond measures 165 feet x 65 feet x 5 feet deep and has 53,625 cubic feet of rearing space. The normal loading of 320,000 fish produces the best looking smolts and a DI significantly less than 0.3. The maximum design capacity is 500,000 fish with a DI of 0.092. Water flow through this pond is 6.24 cfs. A catwalk across the length of the pond supports eight automated Nielson feeders.

Red River - A 170-foot x 70-foot x 4-foot-6 inch deep rearing pond will rear a maximum of 320,000 Chinook smolts. The maximum design capacity is 500,000 fish with a DI of 0.092. Water flow through this pond is 6.24 cfs. This pond has a hypalon plastic liner with eight to ten inch diameter cobblestones on the inclined banks. The bottom of the pond is a bare liner, which aids in pond vacuuming. A catwalk runs the entire length of the rearing pond and holds eight automated Nielson feeders. Water flow through the pond is 4.09 cfs.

Hatchery and satellite water temperatures are monitored constantly with recording thermographs and checked routinely with hand held thermometers. Early rearing water temperatures (vat room) typically range from 4.4ºC to 13.3ºC. Dissolved oxygen and total dissolved gas are monitored monthly using hand held meters. Dissolved oxygen typically remains at 8.0 ppm or greater. Total dissolved gas typically averages 100%.

During early rearing, vats are cleaned daily and dead fish removed. During final rearing, outside raceways are cleaned every other day but dead fish are removed daily.

9.2.4 Indicate biweekly or monthly fish growth information (average program performance), including length, weight, and condition factor data collected during rearing, if available.

Juvenile spring Chinook salmon are sample-counted monthly. Fish length and weight are recorded. Condition factor and conversion rate are calculated. See Table 22 below.

9.2.5 Indicate monthly fish growth rate and energy reserve data (average program performance), if available.

Growth information (monthly length increase) for spring Chinook salmon reared at the Clearwater Fish Hatchery is presented below (Table 21). Data is IDFG unpublished information and represents the average monthly growth from 1994-2008.

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Table 21. Average monthly growth of spring Chinook reared at Clearwater Hatchery 1994-2008. Month in Culture Growth Increase Per Month (cm) December 0.15 January 0.20 February 0.46 March 0.53 April 0.99 May 0.99 June 1.14 July 0.91 August 0.94 September 0.74 October 0.71 November 0.69 December 0.56 January 0.48 February 0.61 March 0.41

9.2.6 Indicate food type used, daily application schedule, feeding rate range (e.g., % B.W./day and lbs/gpm inflow), and estimates of total food conversion efficiency during rearing (average program performance)

During early rearing, spring and summer Chinook salmon are fed a Bio-Oregon formula diet. Fish are fed every hour during this stage of development using automated feeders. Feeding rates range from 5.0% to 1.8% body weight per day. The average feed conversion rate during the early rearing period is 0.97 pounds of feed for every pound of weight gain.

During final rearing in outside raceways, spring Chinook salmon are fed BioOregon’s grower diet. Fish are fed every hour during this stage of development using pneumatic system. Feeding rates range from 2.0 to 1.8% body weight per day. The average feed conversion rate during this stage of development is 1.3 pounds of feed for every pound of weight gain.

9.2.7 Fish health monitoring, disease treatment, and sanitation procedures

At spawning, all spring Chinook salmon are screened for bacterial and viral pathogens. Eggs from females positive for bacterial kidney disease Renibacterium salmoninarum (BKD) are culled to an acceptable risk level established annually by all stakeholders.

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During rearing at Clearwater Fish Hatchery, regular fish health inspections are conducted. If disease agents are suspected or identified, more frequent inspections will be conducted. Recommendations for treating specific disease agents comes from the Idaho Department of Fish and Game Fish Health Laboratory in Eagle, ID.

Prior to release, the Eagle Fish Health Laboratory conducts a final pre-release fish health inspection.

9.2.8 Smolt development indices (e.g., gill ATPase activity), if applicable

No smolt development indices are developed in this program.

9.2.9 Indicate the use of "natural" rearing methods as applied in the program

No semi-natural or natural rearing objectives are applied during Chinook salmon incubation or rearing at the Clearwater Fish Hatchery. Acclimation ponds are used for some but not all juveniles released from this program.

9.2.10 Indicate risk aversion measures that will be applied to minimize the likelihood for adverse genetic and ecological effects to listed fish under propagation

ESA-listed, wild/natural spring Chinook salmon are not propagated at the Clearwater Fish Hatchery.

SECTION 10. RELEASE

In this section, fish release levels and release practices applied through the hatchery program are described.

10.1 PROPOSED FISH RELEASE LEVELS

Table 22. Life stage, location, marking protocol and numbers of Chinook released from Clearwater Hatchery. LIFE STAGE and RUN RELEASE ANNUAL RELEASE LEVEL TYPE LOCATION Eyed Eggs 0 Unfed Fry 0 Fry 0 (Parr) Upper Fingerling (Spring CH) Selway River 300,000 No Clip/OTC Mark Yearlings Transfer to NPTH 200K; 66K Ad/CWT, 134K CWT only Full Term Smolt (Spring Lower Selway CH) River 400K; 145K AD, 120K Ad/CWT, 135K CWT only, 17,100 PIT

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Table 22 Continued Full Term Smolt (Spring Release moved to Red River to accommodate Summer CH run at CH) Crooked River Crooked River Full Term Smolt (Spring CH) Red River 1.1 Mil; 100% Ad, 120K Ad/CWT, 21,500 PIT Full Term Smolt (Spring CH) Powell 400K; 100% Ad, 120K Ad/CWT, 17,100 PIT Full Term Smolt (Spring CH) Clear Creek 235K; 100% Ad, 120K Ad/CWT, 17,100 PIT Full Term Smolt Lower Crooked 200-600K; 100% CWT No Ad clip. In the future Ad clip will be added (Summer CH) River when Run is self supporting

10.2 SPECIFIC LOCATION(S) OF PROPOSED RELEASE(S)

Stream, river, or watercourse:

Stream: Powell Satellite (Walton Creek) Release Point (EPA Number): 170603030270 Major Watershed: Lochsa River Basin or Region: Snake River

Stream: Crooked River Satellite Release Point (EPA Number): 170603050330 Major Watershed: South Fork Clearwater River Basin or Region: Snake River

Stream: Red River Satellite Release Point (EPA Number): 170603050350 Major Watershed: South Fork Clearwater River Basin or Region: Snake River

Stream: Upper Selway River Release Point (EPA Number): 1706030101301 Major Watershed: Selway River Basin or Region: Snake River

Stream: Lower Selway River Release Point (EPA Number): 176030200400 Major Watershed: Selway River Basin or Region: Snake River

Stream: Clear Creek Release Point (EPA Number): 1706030400100 Major Watershed: Clearwater River Basin or Region: Snake River

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10.3 ACTUAL NUMBERS AND SIZES OF FISH RELEASED BY AGE CLASS THROUGH THE PROGRAM

Table 23. Number and size of Chinook released from Clearwater Hatchery by age class, 1998-2008. Release Eggs/ Unfed year Fry Avg size Fry Avg size Fingerling Avg size Yearling Avg size 1998 0 806,057 17 1999 1,223,153 100 1,987,308 15 – 25 2000 1,475,862 17 2001 174,191 21.1 607,632 12.5 2002 1,427,762 31 2,353,118 15.8 2003 1,649,175 50.8 2,037,506 21.55 2004 882,950 47 1,538,156 15.83 2005 474,300 20.9 1,505,666 15.7 2006 648,827 25.09 1,914,079 16.28 2007 n/a 1,670,006 15.63 2008 937,616 37.9 1,666,315 16.74 2009 432,148 60.5 2,145,538 16.63

10.4 ACTUAL DATES OF RELEASE AND DESCRIPTION OF RELEASE PROTOCOLS

Table 24. Clearwater Hatchery release dates for Chinook fingerlings and yearlings, 1996-2009. Year Year Life Stage Date Released Life Stage Date Released Released Released Fingerling 1996 n/a Yearling 1997 4/19-5/19 Fingerling 1997 n/a Yearling 1998 4/11-4/15 Fingerling 1998 7/7, 8/5 Yearling 1999 3/16-4/13 Fingerling 1999 n/a Yearling 2000 3/19-4/7 Fingerling 2000 9/28 Yearling 2001 3/29-4/13 Fingerling 2001 n/a Yearling 2002 4/9/2012 Fingerling 2002 7/31; 8/4-21; 9/27-30 Yearling 2003 3/21-4/3 Fingerling 2003 7/28-29; 9/16-26 Yearling 2004 3/25-4/9 Fingerling 2004 9/23-9/26 Yearling 2005 3/21-4/5 Fingerling 2005 6/21-29; 9/16-18 Yearling 2006 3/22-4/6 Fingerling 2006 n/a Yearling 2007 3/23/-4/6 Fingerling 2007 6/23-6/30; 9/10-9/27 Yearling 2008 3/19-4/9 Fingerling 2008 6/23-6/30; 9/10 Yearling 2009 3/23-4/9

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10.5 FISH TRANSPORTATION PROCEDURES, IF APPLICABLE

All fish reared at the Clearwater Hatchery are transported off station for release in the upper basin of the Clearwater drainage. Fish are loaded into transport trucks using a Magic Valley Heliarc fish pump. The loading density guideline for transport vehicles is 0.5 pound of fish per gallon of water. The transport tanks are insulated to maintain good temperature control. Each tank is fitted with an oxygen system and fresh flow agitators. Maximum transport time is approximately 3-4 hours.

10.6 ACCLIMATION PROCEDURES (METHODS APPLIED AND LENGTH OF TIME)

Releases at Crooked River, lower Selway River and Clear Creek are acclimated for one hour in the truck prior to release. One half of the water in the truck tank is drained and replaced with water from the release site for acclimation. Releases at Powell and Red River are acclimated for four hours to ten days depending on weather conditions.

10.7 MARKS APPLIED, AND PROPORTIONS OF THE TOTAL HATCHERY POPULATION MARKED, TO IDENTIFY HATCHERY ADULTS

All general production harvest mitigation fish are marked with an adipose fin clip. Fish released as part of a supplementation effort have intact adipose fins but are coded-wire tagged. All Chinook salmon released from the Clearwater Fish Hatchery are marked or tagged to allow differentiation from natural-origin fish. The one exception to this are the parr released into the Upper Selway River which are marked with Oxytetracycline. See Table 22 for a list of mark types for each of the Clearwater Fish Hatchery Chinook salmon releases. The number of juveniles produced to meet supplementation objectives are specified in the 2008-2017 US v. Oregon Management Agreement. Annual in-season broodstock planning is adapted to actual adult returns for each brood year.

10.8 DISPOSITION PLANS FOR FISH IDENTIFIED AT THE TIME OF RELEASE AS SURPLUS TO PROGRAMMED OR APPROVED LEVELS

If juveniles are produced in excess of 10% of the programmed release, the IDFG will consult with the Nez Perce Tribe, USFW, and NMFS to develop an alternative location that poses low risk to natural anadromous and resident species, but still allows some contribution to the LSRCP program.

10.9 FISH HEALTH CERTIFICATION PROCEDURES APPLIED PRE- RELEASE

Between 45 and 30 days prior to release, a 20-fish pre-liberation sample is taken from each rearing lot to assess the prevalence of viral replicating agents and to detect the pathogens responsible for bacterial kidney disease and whirling disease. In addition, an organosomatic index is developed for each release lot. Diagnostic services are provided by the IDFG Eagle Fish Page 57

Health Laboratory.

10.10 EMERGENCY RELEASE PROCEDURES IN RESPONSE TO FLOODING OR WATER SYSTEM FAILURE

Emergency procedures are in place to guide activities in the event of a potential catastrophic event. Plans at the Clearwater Fish Hatchery include a trouble-shooting and repair process followed by the implementation of an emergency action plan if the problem cannot be resolved. Actions include fish consolidations and if necessary fish will be released directly to the Clearwater River.

Satellite facilities have similar plans in place. At these sites, it is generally easy to release fish directly to receiving waters if the emergency cannot be corrected.

10.11 INDICATE RISK AVERSION MEASURES THAT WILL BE APPLIED TO MINIMIZE THE LIKELIHOOD FOR ADVERSE GENETIC AND ECOLOGICAL EFFECTS TO LISTED FISH RESULTING FROM FISH RELEASES

Actions taken to minimize adverse effects on listed fish include:

Continuing fish health practices to minimize the incidence of infectious disease agents. Follow IHOT, AFS, and PNFHPC guidelines.

Marking hatchery-produced spring Chinook salmon for broodstock management. Smolts released for supplementation research will be marked differentially from other hatchery production fish.

Continuing to reduce effect of the release of large numbers of hatchery Chinook salmon at a single site by spreading the release over a number of days by trucking strategy or volitional release from ponds.

Attempting to program time of release to mimic natural fish for Clearwater River supplementation research releases, given the constraints of the hatchery and its transportation system.

Continuing to use broodstock for general production and supplementation research that exhibit life history characteristics similar to locally evolved stocks.

Continuing to segregate female spring Chinook salmon broodstock for BKD via ELISA. We will incubate each female's progeny separately and also segregate progeny for rearing. We will continue development of culling and rearing segregation guidelines and practices, relative to BKD.

Monitoring hatchery effluent to ensure compliance with National Pollutant Discharge Elimination System permit.

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Continuing Hatchery Evaluation Studies (HES) to provide comprehensive monitoring and evaluation for LSRCP Chinook.

SECTION 11. MONITORING AND EVALUATION OF PERFORMANCE INDICATORS

11.1.1 Describe plans and methods proposed to collect data necessary to respond to each Performance Indicator identified for the program

In section 11.1.1 below, a series of tables, each followed by narrative, are provided for the purpose of adding detail with regards to plans and methods used to collect data necessary to respond to indicators listed in Section 1.10. Additionally, two columns are provided in the tables to indicate whether each indicator is:

1. Applicable to the hatchery program/s described in this HGMP (yes “Y” or no “N”) 2. Currently being monitored. a. For cells with a “Y”, the indicator is being monitored with funding provided by the hatchery mitigation program. b. For cells with a “C”, the indicator is being monitored, but is tied to a separately funded program (e.g. Idaho Supplementation Studies (ISS), Idaho Natural Production Monitoring Program (INPM), General Parr Monitoring (GPM) program etc.). Without continued funding for these programs, many of the M&E components will not occur. For example, the ISS program is scheduled to end in 2014 with some components ending in 2012. Funding to offset this loss needs to be identified to avoid significant M&E data gaps. c. For cells with a “Y/C”, the indicator is being monitored and is partially funded through the hatchery mitigation program. Other programs, such as those listed in 2b above, provide the remaining funding. d. For cells with an “N”, the indicator is not currently being monitored. For all indicators applicable to this HGMP that are not being addressed (N), a brief narrative is provided in Section 11.1.2 describing why the particular indicator is not being monitored.

Table 25, at the end of Section 11.1.1, provides a more detailed description of methodologies used in the basin that are more specific to VSP parameters.

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11.1.1 Monitoring and evaluation of “Performance Indicators” presented in Section 1.10.

Category Standards Indicators

Applicable Monitored 1.1.1. Total number of fish harvested in Tribal Y C 1.1. Program contributes to fulfilling tribal fisheries targeting this program. trust responsibility mandates and 1.1.2. Total fisher days or proportion of Y C

treaty rights, as described in harvestable returns taken in Tribal resident

applicable agreements such as under fisheries, by fishery. U.S. v. OR and U.S. v. Washington. 1.1.3. Tribal acknowledgement regarding Y C fulfillment of tribal treaty rights. 1.2.1. Number of fish released by program, Y Y 1.2. Program contributes to mitigation returning, or caught , as applicable to given requirements.

mitigation requirements. LEGAL LEGAL MANDATES 1.3. Program addresses ESA 1.3.1. Section 7, Section 10, 4d rule and annual Y Y

responsibilities. consultation 1.

1.1.1 – 1.1.2 The Nez Perce Tribe (NPT) and the Shoshone/Bannock Tribe (SBT) each authorize and manage fisheries. Both are non-selective fisheries that harvest both hatchery and natural returns. Each tribe conducts statistically based inseason fishery interview programs to estimate fishing effort, numbers of hatchery and natural origin Chinook salmon harvested and other species harvested, IDFG conducts similar statistically based harvest monitoring programs for non-Treaty recreational fisheries. For Chinook salmon fisheries IDFG and Tribal co-managers confer through scheduled inseason conferences to assess current ESA take and harvest shares. Steelhead fisheries are more protracted then Chinook salmon fisheries and require less inseason consultation. IDFG and Tribal co-managers share pre-season fisheries management plans and post- season estimates of harvest and ESA take.

1.1.3 – 1.2.1 Numbers of spring/summer Chinook salmon marked, tagged and total numbers released are in accordance with the production schedule in the 2008-2017 US vs.OR Management Agreement. Fisheries harvests in Idaho are not governed by terms of the US vs. OR agreement but Idaho and the respective Treaty Tribes manage in accordance with the principal of 50% Tribal and 50% non-tribal sharing of fish available for harvest in Idaho fisheries.

The mitigation objectives for the hatchery programs in Idaho are stipulated in the LSRCP and in the 1980 Hells Canyon Settlement Agreement. Each hatchery reports numbers of fish released by life stage in annual run or brood year reports. Representative sub-samples of fish released are code-wire tagged and PIT tagged to assess harvest contribution by release group and survival to the project area upstream of Lower Granite Dam. The majority of fish PIT tagged are representative of the run at large though the FCRPS. PIT tags detected among subsequent adult returns in the fish ladder at Lower Granite Dam are used to estimate in-season total facility specific returns to Lower Granite Dam. An independent estimate of the adult return over Lower Granite Dam is also complete post- season based on summed tribal and non-tribal harvest estimates and hatchery trapping data.

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1.3.1 ESA consultation(s) under Section 7 have been completed, Section 10 permits have been issued, or HGMP has been determined sufficient under Section 4(d), as applicable. Section 7 consultation with USFWS (April 2, 199) resulted in NMFS Biological Opinion for the Lower Snake River Compensation Program (now expired). In 2003, consultation was initiated to develop a new Snake River Hatchery Biological Opinion. Consultation has not been completed. Section 10 Permit Numbers 919 – East Fork Salmon River Satellite Facility, 920 – Sawtooth Fish Hatchery, and 921 – McCall Fish Hatchery, authorized direct and indirect take of listed Snake River salmon associated with hatchery operations and broodstock collection at Lower Snake River Compensation Program hatcheries operated by Idaho Department of Fish and Game. Expired 12/31/98; reapplication (to consolidate all programs under permit 1179) in process. Section 10 Permit Number 922 authorized direct take of listed Snake River salmon associated with hatchery operations and broodstock collection at the Idaho Power Company Pahsimeroi Hatchery operated by Idaho Department of Fish and Game. Expired 12/31/98; reapplication in process. Section 10 Permit Number 903 authorized indirect take of listed Snake River salmon associated with hatchery operations and broodstock collection at Idaho Power Company mitigation hatcheries operated by Idaho Department of Fish and Game, including Rapid River hatchery, Oxbow Fish Hatchery/Hell’s Canyon Trap and Pahsimeroi Hatchery. Expired 12/31/98; reapplication in process. Section 10 Permit Number 1120 authorized annual take of listed sockeye salmon associated continuation of a sockeye salmon captive broodstock program. Expired 12/31/2002; reapplication (under Permit 1454) in process.

Anadromous hatchery programs managed by IDFG have operated based on annual acknowledgement from NOAA Fisheries that the programs are in compliance with the provisions of Section 10 (# 1179) that expired in 1999. Newly developed program specific HGMPs are currently under review.

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Category Standards Indicators

Applicable Monitored 2.1.1. Hatchery is operated as a segregated program. Y Y 2.1. Confirmation of hatchery 2.1.2. Hatchery is operated as an integrated program type 2.1.3. Hatchery is operated as a conservation program Y Y 2.2. Hatchery - natural 2.2.1. Hatchery fish can be distinguished from natural Y Y composition of hatchery fish in the hatchery broodstock and among broodstock and natural spawners in supplemented or hatchery spawners are known and influenced population(s) consistent with hatchery type. 2.3.1. Hatchery and natural-origin adult returns can be Y Y/C adequately forecasted to guide harvest 2.3. Restore and maintain opportunities. treaty-reserved tribal and 2.3.2. Hatchery adult returns are produced at a level of Y Y non-treaty fisheries. abundance adequate to support fisheries in most years with an acceptably limited impact to natural-spawner escapement. 2.4. Fish for harvest are 2.4.1. Number of fish release by location estimated and Y Y produced and released in in compliance with AOPs and US vs. OR a manner enabling Management Agreement. effective harvest, as 2.4.2. Number of adult returns by release group Y Y described in all applicable harvested fisheries management 2.4.3. Number of non-target species encountered in Y Y plans, while avoiding over- fisheries for targeted release group. harvest of non-target species. 2.5.1. Juvenile rearing densities and growth rates are Y Y 2.5. Hatchery incubation, monitored and reported. rearing, and release 2.5.2. Numbers of fish per release group are known Y Y practices are consistent and reported. with current best 2.5.3. Average size, weight and condition of fish per Y Y management practices for release group are known and reported. the program type. 2.5.4. Date, acclimation period, and release location of Y Y each release group are known and reported. 2.6.1. Production adheres to plans documents Y Y developed by regional co-managers (e.g. US vs. OR Management agreement, AOPs etc.). 2.6.2. Harvest management, harvest sharing Y 2.6. Hatchery production, Y agreements, broodstock collection schedules, harvest management, and and disposition of fish trapped at hatcheries in IMPLEMENTATIONAND COMPLIANCE monitoring and evaluation excess of broodstock needs are coordinated of hatchery production are

2. among co-management agencies. coordinated among 2.6.3. Co-managers react adaptively by consensus to affected co-managers. Y Y monitoring and evaluation results.

2.6.4. Monitoring and evaluation results are reported to co-managers and regionally in a timely Y fashion. Y

2.1.1 – 2.1.3 Each hatchery program has a defined purpose relative to mitigation and conservation.

2.2.1- 2.6.4 The adipose fin-clip is the primary mark that we use distinguish hatchery origin from natural origin fish in harvests and escapement . All hatchery releases for harvest mitigation are adipose fin-clipped and representative portions of those releases are coded-wire tagged. Relatively small numbers of releases of Chinook salmon intended to supplement natural populations are released with intact adipose fins but are coded-wire

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tagged. Steelhead intended to supplement natural populations are also released un- clipped. Few of these releases are coded-wire tagged. The marking rate by mark type for each release group of Chinook salmon and steelhead are inventories and reported annually.

Representative sub-samples of fish released from anadromous fish hatcheries in Idaho are code-wire tagged and PIT tagged to assess harvest contribution by release group. Coded- wire tag recovery data indicate that harvest of Snake River spring/summer Chinook salmon and steelhead are negligible in ocean fisheries. ODFW, WDFW, and CRITFC conduct statistically based fishery, interview biological sampling, and tag recovery programs in Tribal and non-Tribal fisheries in the mainstem and tributaries of the Columbia River in zones 1 through 6 and in the lower Snake River below Lower Granite Dam. Data from these sampling programs are used to estimate fishing effort, numbers of hatchery and natural origin fish harvested and released and in many cases contributions of specific mitigation hatchery releases to harvest. Results from these program are available in-season to assist harvest and hatchery managers and are reported in summary jointly by ODFW and WDFW.

IDFG, Nez Perce Tribe (NPT) and the Shoshone/Bannock Tribe (SBT) each authorize and manage fisheries in the boundary waters of the Snake River and in mainstems and tributaries of the Snake, Clearwater and Salmon Rivers. ODFW and WDFW also conduct recreational fisheries in the boundary waters of the Snake River shared by Idaho. Non- Tribal recreational fisheries are selective for adipose fin-clipped hatchery origin fish. Tribal fisheries are largely non-selective fisheries that harvest both hatchery and natural returns. IDFG, ODFW, WDFW and Tribes conducts statistically based in-season and post season fishery interview programs to estimate fishing effort, numbers of hatchery and natural origin fish harvested and released and other species encountered. Coded-wire tag recovery data from these programs are used to estimate hatchery specific contributions to age specific harvests by fishery.

IDFG and the Tribes estimate annual escapements of natural populations that are affected by fisheries targeting program fish through weirs operated in conjunction with hatchery programs. Statewide index counts of Chinook salmon redds are conducted to estimate numbers of spawners by population. IDFG and the Tribes have developed genetic stock identification standard and a sampling program at Lower Granite Dam to estimate escapement above the dam at the level of major spawning population groups for both Chinook salmon and steelhead.

Hatchery release numbers, mark rates among releases and sampling rates in Snake River and Columbia River mainstem and tributary fisheries downstream of Lower Granite Dam are reported by ODFW, WDFW, and CRITFC co-managers in the RMIS database maintained by the Pacific Sates Marine Fisheries Commission. IDFG, Nez Perce Tribe (NPT) and the Shoshone/Bannock Tribe (SBT) each authorize and manage fisheries in the boundary waters of the Snake River and mainstems and tributaries of the Snake, Clearwater and Salmon Rivers. ODFW and WDFW also conduct recreational fisheries in the boundary waters of the Snake River shared by Idaho. Non-Tribal recreational fisheries are selective for adipose fin-clipped hatchery origin fish. Tribal fisheries are largely non-selective fisheries that harvest both hatchery and natural returns. IDFG, Page 63

ODFW, WDFW and Tribes conducts statistically based in-season and post season fishery interview programs to estimate fishing effort, numbers of hatchery and natural origin fish harvested and released and other species encountered. Sampling rate by mark type, number of marks by program observed in fishery samples, and estimated total contribution of each population to by fishery are estimated and reported annually.

For hatchery Chinook salmon populations, IDFG completed annual run reconstructions based on population and age specific harvest estimates in Columbia River, Snake River and Snake River tributary fisheries and age specific rack returns. Run reconstruction data for each hatchery are used to develop hatchery specific pre-season run forecasts. Natural returns to Idaho are forecasted using similar run reconstructions of aggregate Snake River natural returns to Lower Granite Dam. IDFG and Tribal co-managers in the Snake Basin plan fisheries based on these forecasts. IDFG and Tribal co-managers confer through scheduled in-season conferences to assess accuracy of the preseason forecast based on in- season estimates of the actual hatchery returns from real-time PIT tag detections in the Columbia River hydro-system. Co-managers also assess inseason estimates of ESA take, harvest shares, and the disposition of hatchery returns to racks in excess of broodstock needs.

Steelhead fisheries are more protracted then Chinook salmon fisheries and require less in- season consultation. IDFG and Tribal co-managers share pre-season fisheries management plans and post-season estimates of harvest and ESA take.

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Category Standards Indicators

Applicable Monitored 3.1. Release groups are marked in a 3.1.1. All hatchery origin fish recognizable by mark Y Y manner consistent with or tag and representative known fraction of information needs and protocols each release group marked or tagged for monitoring impacts to natural- uniquely. and hatchery-origin fish at the 3.1.2. Number of unique marks recovered per Y Y targeted life stage(s)(e.g. in monitoring stratum sufficient to estimate juvenile migration corridor, in number of unmarked fish from each release fisheries, etc.). group with desired accuracy and precision. 3.2.1. Abundance of fish by life stage is monitored Y C annually. 3.2.2. Adult to adult or juvenile to adult survivals Y C are estimated. 3.2.3. Temporal and spatial distribution of adult Y C 3.2. The current status and trends of spawners and rearing juveniles in the natural origin populations likely to freshwater spawning and rearing areas are be impacted by hatchery monitored.

production are monitored. 3.2.4. Timing of juvenile outmigration from rearing

areas and adult returns to spawning areas Y C are monitored. 3.2.5. Ne and patterns of genetic variability are frequently enough to detect changes across Y C generations.

TIONPROGRAMS 3.3.1. Number of fish release by location estimated Y Y 3.3. Fish for harvest are produced and and in compliance with AOPs and US vs. OR released in a manner enabling Management Agreement. effective harvest, as described in all 3.3.2. Number of adult returns by release group applicable fisheries management Y Y harvested plans, while avoiding over-harvest 3.3.3. Number of non-target species encountered of non-target species. Y Y in fisheries for targeted release group. 3.4.1. Fraction of strays among the naturally Y C 3.4. Effects of strays from hatchery spawning fish in non-target populations. programs on non-target (un- 3.4.2. Fraction of strays in non-target populations Y C supplemented and same species) that originate from in-subbasin releases. populations remain within 3.4.3. Fraction of hatchery strays in out-of-basin Y C acceptable limits. natural population. 3.5.1. Temporal and spatial trends in habitat Y N 3.5. Habitat is not a limiting factor for capacity relative to spawning and rearing for the affected supplemented target population. population at the targeted level of 3.5.2. Spatial and temporal trends among adult Y C supplementation. spawners and rearing juvenile fish in the available habitat. 3.6.1. Pre- and post-supplementation trends in Y C abundance of fish by life stage is monitored annually. 3.6.2. Pre- and post-supplementation trends in Y C 3.6. Supplementation of natural adult to adult or juvenile to adult survivals population with hatchery origin are estimated. production does not negatively 3.6.3. Temporal and spatial distribution of natural Y C impact the viability of the target origin and hatchery origin adult spawners population. and rearing juveniles in the freshwater spawning and rearing areas are monitored.

HATCHERY EFFECTIVENESSMONITORING FOR AUGMENTATION SUPPLEMENTAAND 3.6.4. Timing of juvenile outmigrations from Y C

rearing area and adult returns to spawning 3. areas are monitored.

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Category Standards Indicators

Applicable Monitored 3.7.1. Adult progeny per parent (P:P) ratios for Y Y/C hatchery-produced fish significantly exceed those of natural-origin fish. 3.7.2. Natural spawning success of hatchery-origin Y N fish must be similar to that of natural-origin fish. 3.7.3. Temporal and spatial distribution of Y C 3.7. Natural production of target hatchery-origin spawners in nature is similar population is maintained or to that of natural-origin fish. enhanced by supplementation. 3.7.4. Productivity of a supplemented population is Y C similar to the natural productivity of the population had it not been supplemented (adjusted for density dependence). 3.7.5. Post-release life stage-specific survival is Y C similar between hatchery and natural-origin population components. 3.8.1. Adult life history characteristics in Y C supplemented or hatchery influenced populations remain similar to characteristics 3.8. Life history characteristics and observed in the natural population prior to patterns of genetic diversity and hatchery influence. variation within and among natural 3.8.2. Juvenile life history characteristics in Y C populations are similar and do not supplemented or hatchery influenced change significantly as a result of populations remain similar to characteristics hatchery augmentation or in the natural population those prior to supplementation programs. hatchery influence. 3.8.3. Genetic characteristics of the supplemented Y C population remain similar (or improved) to the un-supplemented populations. 3.9.1. Genetic characteristics of hatchery-origin Y C fish are similar to natural-origin fish. 3.9. Operate hatchery programs so that 3.9.2. Life history characteristics of hatchery-origin Y C life history characteristics and adult fish are similar to natural-origin fish. genetic diversity of hatchery fish 3.9.3. Juvenile emigration timing and survival Y C mimic natural fish. differences between hatchery and natural- origin fish are minimized. 3.10. The distribution and incidence of 3.10.1 Detectable changes in rate of occurrence and Y N diseases, parasites and pathogens spatial distribution of disease, parasite or in natural populations and hatchery pathogen among the affected hatchery and populations are known and natural populations. releases of hatchery fish are designed to minimize potential spread or amplification of diseases, parasites, or pathogens among natural populations.

3.1.1 – 3.9.3 The adipose fin-clip is the primary mark that we use distinguish hatchery origin from natural origin fish in harvests and escapement. All hatchery releases for harvest mitigation are adipose fin-clipped and representative portions of those releases are coded-wire tagged. Relatively small numbers of releases of Chinook salmon intended to supplement natural populations are released un-clipped but are coded-wire tagged. Steelhead intended to supplement natural populations are also released un-clipped. Few of these releases are coded-wire tagged. The marking rate by mark type for each release group of Chinook salmon and steelhead are inventories and reported annually.

Hatchery release numbers, mark rates among releases and sampling rates in Snake River

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and Columbia River mainstem and tributary fisheries downstream of Lower granite Dam are reported by ODFW, WDFW, and CRITFC co-managers in the RMIS database maintained by the Pacific Sates Marine Fisheries Commission. IDFG, Nez Perce Tribe (NPT) and the Shoshone/Bannock Tribe (SBT) each authorize and manage fisheries in the boundary waters of the Snake River and mainstems and tributaries of the Snake, Clearwater and Salmon Rivers. ODFW and WDFW also conduct recreational fisheries in the boundary waters of the Snake River shared by Idaho. Non-Tribal recreational fisheries are selective for adipose fin-clipped hatchery origin fish. Tribal fisheries are largely non-selective fisheries that harvest both hatchery and natural returns. IDFG, ODFW, WDFW and Tribes conducts statistically based in-season and post season fishery interview programs to estimate fishing effort, numbers of hatchery and natural origin fish harvested and released and other species encountered. Sampling rate by mark type, number of marks by program observed in fishery samples, and estimated total contribution of each population to by fishery are estimated and reported annually

Numbers of spawners by age are estimated annually by weir counts, spawning ground surveys or a combination of both methods for all Chinook salmon conservation programs. All fish passed upstream of weirs are identified by marks or tags as hatchery or natural origin and are sampled for age, sex, and size. Index redd counts are conducted on all natural spawning areas affected by supplementation programs and representative portions of carcasses on spawning grounds are sampled for marks, or tags and for age, sex, and size information. Annual estimated of spawners by age are used to monitor inter-annual spawner-recruit trends.

Because steelhead migration into spawning areas in Idaho coincides with high flows it is not possible to accurately estimate total spawning escapement in supplemented streams using weir counts or spawning ground surveys. Partial escapement estimated from weirs on the upper reaches of spawning areas are available for each supplemented system but escapements to lower reaches cannot be measured. Additional funding will be required to build permanent weirs below spawning areas on supplemented systems. Additional funding is also required to implement parental based tagging programs to distinguish progeny from hatchery origin from natural origin spawners in these systems.

Releases of fish from supplementation programs are marked or tagged to differentiate them from fish released for harvest mitigation and from natural origin fish. Mark rate by mark type for all releases are inventoried and reported. Screw traps are used to estimate numbers natural origin out-migrants from the supplemented population. All fish passed upstream of weirs are identified by marks or tags as hatchery or natural origin and are sampled for age, sex, and size. Index redd counts are conducted on all natural spawning areas affected by supplementation programs and representative portions of carcasses on spawning grounds are sampled for marks, or tags and for age, sex, and size information. Annual estimated of spawners by age are used to monitor inter-annual spawner-recruit trends.

While the above methods allow us to estimate numbers of natural origin and hatchery origin spawners on the spawning grounds, they do not allow us to estimate the relative contribution of hatchery and natural spawners to natural production. IDFG, Tribal and federal co-managers in the Snake basin are currently collecting genetic samples from all Page 67

fish spawned in anadromous hatcheries and all natural and hatchery fish passed above weirs associated with hatchery programs. IDFG has worked in conjunction with CRITFC to build a library of genetic markers that can be used to identify individual parents of juveniles produced by adults sampled in hatchery broodstocks or from adults passed above weirs to spawn. Parental based analysis of juvenile production can be used to assess the relative contributions of individual spawning crosses (i.e. hatchery x hatchery, hatchery x natural, or natural x natural). While we currently have the samples in hand to do this analysis and will continue to collect those samples, we have no funding to process the samples for parental analysis.

Hatcheries or hatchery satellite facilities where broodstocks are collected are typically located on the tributary where the parent natural population for the hatchery broodstock resides. Hatchery and natural returns at those locations are trapped and enumerated at weirs run throughout the adult migration. Long time series of historic daily migration data are available at all facilities for both hatchery and natural returns. Managers use historic data to construct timing curves of average daily proportion of the run by date. These timing curves are used to project the numbers of natural fish returning to the weir and the numbers of the proportion of the annual broodstock need that should be collected by day. All hatchery and natural fish captured at the weirs are sampled for age, sex, and size data. Age is typically determined by length frequency analysis using age length relationships from known age coded-wire tagged fish.

All natural fish intercepted at hatchery facilities where broodstocks are maintained as a segregated population, all natural fish trapped during broodstock collection are released to spawn naturally in the available habitat upstream of the weir. At hatchery programs where integrated broodstock are maintained or are being developed, the natural and hatchery composition of the broodstock and the affected natural populations are carefully monitored and controlled based sliding scales specific to each program. The proportions of natural fish into the hatchery broodstock and hatchery fish into the natural spawning population are based on a sliding scale of natural abundance. Success of the program is predicated on an average measure of percent natural influence in the hatchery and natural populations across generations.

The overwhelming majority of hatchery produced spring/summer Chinook salmon and all steelhead in Idaho are released as smolts. Representative portions of all smolt releases are PIT tagged and migratory timing of these fish is known. Hatchery smolts quickly exit terminal tributary rearing areas. While mainstem migration among hatchery smolts corresponds with typical timing observed among natural origin fish no significant competitive interactions during their brief seaward migratory period have been documented.

Where parr and presmolt release programs and egg box programs are implemented in some areas where natural production is severely depressed. The size of these programs are small and metered by best available estimates of the abundance of natural fish and habitat capacity.

At all broodstock collection sites for spring/summer Chinook salmon hatcheries and steelhead hatcheries operated by Idaho Department of Fish and Game, daily records of Page 68

adult fish trapped and their disposition (i.e. held for brood, passed above weir to spawn, etc.) are maintained. Representative fractions of all natural origin and hatchery fish trapped are sampled for age, sex and size. Daily spawning records, incubator loading densities, survival at various stages of development, and fry emergence timing are documented for each hatchery. Juvenile growth and survival are monitored by life stage and all production fish are adipose fin-clipped and or coded-wire tagged. A representative sample of all smolt release groups are PIT tagged. All data relative to hatchery adult collection, spawning, incubation, and rearing data are stored in a standardized relational data base that is maintained collaboratively with Tribal, Federal and state co-managers in the Snake River Basin. All coded wire and PIT tagging and release data are entered into RMIS and PITAGIS databases maintained by the Pacific States Marine Fisheries Commission. PIT tag detections at key points in the seaward migration of juvenile releases from hatcheries are used to estimate migration timing and survival.

The Idaho Supplementation Studies is a large scale effectiveness monitoring program that is designed to track production and productivity in supplemented (treated) verses un- supplemented (control) streams. It is a long term program that is designed to last approximately 20 years and assess production and productivity prior to, during and after treatment in approximately 15 streams. The study is conducted collaboratively by IDFG, the Nez Perce Tribe, the Shoshone/ Bannock Tribes, and the USFWS. The study collects comparative production and productivity measures in approximately 15 control streams that have been paired with treatment sites and monitored across the duration of the study. Tributaries where Sawtooth, Pahsimeroi, McCall, Clearwater, and Kooskia hatcheries release spring/summer Chinook salmon are among the study sites. At each site, juvenile screw traps assess hatchery and natural juvenile outmigration timing, abundance, age structure, condition and survival. Representative portions of the natural outmigration are PIT tagged to assess timing and survival to Lower Granite Dam. ISS also monitors adult return in treatment streams at weirs and in treatment and control streams by systematic red counts in natural spawning areas through spawning. Weir and redd count data provide data on adult spawn timing, age structure, genetic composition, and spatial distribution.

The Idaho Natural Production Monitoring Program and the Idaho Steelhead Monitoring and Evaluation Study monitor adult and juvenile segments of natural Chinook salmon and steelhead populations other than those included for effectiveness monitoring in the ISS project. Snorkel surveys have historically been conducted in representative standardized index sections of streams where natural populations of Chinook and steelhead spawn and rear. Snorkel surveys provide estimates of relative annual abundance, temporal, and spatial distribution of juvenile salmon and steelhead. Systematic sampling of juveniles for age and tissues for genetic analyses provide estimates of age composition and genetic structure and diversity in each population.

The Idaho Natural Production Monitoring program also oversees the systematic redd count survey program for natural populations of Chinook salmon throughout Idaho. Data from this program are available from the 1950’s through the present and provide data to estimate historic abundance and distribution of spawners in all extant natural populations of Chinook salmon in Idaho. During systematic spawning ground surveys, carcasses of adult spawners are also sampled for scales, sex and size information and for tissues analyzed to characterize the genetic structure of the populations. Page 69

Category Standards Indicators

Applicable Monitored 4.1. Artificial production facilities are 1.1.1 Annual reports indicating level of Y Y operated in compliance with all compliance with applicable standards applicable fish health guidelines and and criteria. facility operation standards and 1.1.2 Periodic audits indicating level of Y Y protocols such as those described compliance with applicable standards by IHOT, PNFHPC, the Co-Managers and criteria. of Washington Fish Health Policy, INAD, and MDFWP. 4.2.1 Discharge water quality compared to Y Y applicable water quality standards and guidelines, such as those described or 4.2. Effluent from artificial production required by NPDES, IHOT, PNFHPC, and facility will not detrimentally affect Co-Managers of Washington Fish Health natural populations. Policy tribal water quality plans, including those relating to temperature, nutrient loading, chemicals, etc. 4.3.1. Water withdrawals compared to Y Y applicable passage criteria. 4.3. Water withdrawals and instream 4.3.2. Water withdrawals compared to NMFS, Y Y water diversion structures for USFWS, and WDFW juvenile screening artificial production facility criteria. operation will not prevent access to 4.3.3. Number of adult fish aggregating Y Y natural spawning areas, affect and/or spawning immediately below spawning behavior of natural water intake point. populations, or impact juvenile 4.3.4. Number of adult fish passing water Y Y rearing environment. intake point. 4.3.5. Proportion of diversion of total stream Y Y flow between intake and outfall. 4.4.1. Certification of juvenile fish health Y Y immediately prior to release, including 4.4. Releases do not introduce pathogens present and their virulence. pathogens not already existing in 4.4.2. Juvenile densities during artificial Y Y the local populations, and do not rearing. significantly increase the levels of 4.4.3. Samples of natural populations for Y N existing pathogens. disease occurrence before and after artificial production releases. 4.5. Any distribution of carcasses or 4.5.1. Number and location(s) of carcasses or Y Y other products for nutrient other products distributed for nutrient enhancement is accomplished in enrichment.

compliance with appropriate 4.5.2. Statement of compliance with Y Y disease control regulations and applicable regulations and guidelines. guidelines, including state, tribal, and federal carcass distribution guidelines. 4.6. Adult broodstock collection 4.6.1. Spatial and temporal spawning Y C operation does not significantly distribution of natural population alter spatial and temporal above and below weir/trap, currently distribution of any naturally and compared to historic distribution. produced population. 4.7.1. Mortality rates in trap. Y Y 4.7. Weir/trap operations do not result 4.7.2. Pre-spawning mortality rates of Y Y in significant stress, injury, or trapped fish in hatchery or after mortality in natural populations. release. 4.8.1. Size at, and time of, release of juvenile Y C 4.8. Predation by artificially produced fish, compared to size and timing of fish on naturally produced fish does natural fish present.

not significantly reduce numbers of 4.8.2. Number of fish in stomachs of sampled N OPERATIONOFARTIFICIAL PRODUCTION FACILITIES natural fish. artificially produced fish, with estimate

of natural fish composition. 4.

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4.1.1 – 4.1.2 https://research.idfg.idaho.gov/Fisheries%20Research%20Reports/Forms/Show%20All% 20Reports.aspx for annual reporting. Reports are available upon request.

4.2.1 https://research.idfg.idaho.gov/Fisheries%20Research%20Reports/Forms/Show%20All% 20Reports.aspx for annual reporting. Permits and compliance reports are available upon request.

4.3.1 – 4.3.5 Water withdrawal permits have been obtained to establish water rights for each hatchery facility. Intake system designed to deliver permitted flows. Operators monitor and report as required. Hatcheries participating in the programs will maintain all screens associated with water intakes in surface water areas to prevent impingement, injury, or mortality to listed salmonids.

4.4.1 – 4.4.3 Certification of fish health conducted prior to release (major bacterial, viral, parasitic pathogens); IDFG fish health professionals sample and certify all release and/or transfer groups.

4.5.1 – 4.5.2 Nutrient enhancement projects, where/when applicable, are outlined in IDFG research, management, and/or hatchery permits and annual reports; see https://research.idfg.idaho.gov/Fisheries%20Research%20Reports/Forms/Show%20All% 20Reports.aspx for annual reporting.

4.6.1 Hatchery and research elements monitor the following characteristics annually: juvenile migration timing, adult return timing, adult return age and sex composition, spawn timing and distribution.

4.7.1 – 4.7.2 Facility will maintain all weirs/traps associated with program to either reduce or eliminate stress, injury, or mortality to listed salmonids. Mortality rates are documented

4.8.1 – 4.8.2 Facility will maintain all weirs/traps associated with program to either reduce or eliminate stress, injury, or mortality to listed salmonids. Mortality rates are documented

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Category Standards Indicators

Applicable Monitored 5.1.1. Total cost of program operation. Y Y 5.1. Cost of program operation does 5.1.2. Sum of ex-vessel value of commercial Y Y not exceed the net economic value catch adjusted appropriately, of fisheries in dollars per fish for all appropriate monetary value of

fisheries targeting this population. recreational effort, and other fishery ECONOMIC - related financial benefits.

5.2. Juvenile production costs are 5.2.1. Total cost of program operation. Y Y EFFECTIVENESS SOCIO comparable to or less than other 5.2.2. Average total cost of activities with Y Y

regional programs designed for similar objectives. 5. similar objectives.

5.1.1 – 5.2.2 Based on surveys completed by the U.S. Fish and Wildlife service within the last decade, anglers in Idaho expend more than $200 million dollars annually on salmon and steelhead fisheries. This is more than an order of magnitude greater than the cost of the program. Production costs per juvenile released in Idaho’s anadromous fish hatcheries are comparable to other programs of similar size and intent in the Columbia River Basin.

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Table 25. Standardized performance indicators and definitions for status and trends and hatchery effectiveness monitoring (Galbreath et al. 2008; appendix C).

Performance Measure Definition

Number of adults (including jacks) that have escaped to a certain point (i.e. - mouth of stream). Population based measure. Calculated with mark recapture methods from weir Adult Escapement to data adjusted for redds located downstream of weirs and in tributaries, and maximum net Tributary upstream approach for DIDSON and underwater video monitoring. Provides total escapement and wild only escapement. [Assumes tributary harvest is accounted for]. Uses TRT population definition where available Number of fish divided by the total number of redds. Applied by: The population estimate Fish per Redd at a weir site, minus broodstock and mortalities and harvest, divided by the total number of redds located upstream of the weir. Number of female spawners divided by the total number of redds above weir. Applied in 2 ways: 1) The population estimate at a weir site multiplied by the weir derived proportion of females, minus the number of female pre-spawn mortalities, divided by the total number Female Spawner per Redd of redds located upstream of the weir, and 2) DIDSON application calculated as in 1 above but with proportion females from carcass recoveries. Correct for mis-sexed fish at weir for 1 above. Counts of redds in spawning areas in index area(s) (trend), extensive areas, and Index of Spawner supplemental areas. Reported as redds and/or redds/km. Abundance - redd counts

In-river: Estimated number of total spawners on the spawning ground. Calculated as the number of fish that return to an adult monitoring site, minus broodstock removals and weir mortalities and harvest if any, subtracts the number of female pre-spawning mortalities and expanded for redds located below weirs. Calculated in two ways: 1) total spawner Spawner Abundance abundance, and 2) wild spawner abundance which multiplies by the proportion of natural origin (wild) fish. Calculations include jack salmon. In-hatchery: Total number of fish actually used in hatchery production. Partitioned by gender and origin. Percent of fish on the spawning ground that originated from a hatchery. Applied in two ways: 1) Number of hatchery carcasses divided by the total number of known origin Hatchery Fraction carcasses sampled. Uses carcasses above and below weirs, 2) Uses weir data to determine number of fish released above weir and calculate as in 1 above, and 3) Use 2 above and carcasses above and below weir. Number of fish caught in ocean and mainstem (tribal, sport, or commercial) by hatchery Ocean/Mainstem Harvest and natural origin. Harvest Abundance in Number of fish caught in ocean and mainstem (tribal, sport, or commercial) by hatchery Tributary and natural origin. Parr abundance estimates using underwater survey methodology are made at pre- Index of Juvenile established transects. Densities (number per 100 m2) are recorded using protocol described Abundance (Density) in Thurow (1994). Hanken & Reeves estimator. Gauss software is (Aptech Systems, Maple Valley, Washington) is used to estimate Juvenile Emigrant emigration estimates. Estimates are given for parr pre-smolts, smolts and the entire Abundance migration year. Calculations are completed using the Bailey Method and bootstrapping for 95% CIs. Gauss program developed by the University of Idaho (Steinhorst 2000). Smolt estimates, which result from juvenile emigrant trapping and PIT tagging, are derived by estimating the proportion of the total juvenile abundance estimate at the tributary comprised of each juvenile life stage (parr, presmolt, smolt) that survive to first mainstem dam. It is calculated by multiplying the life stage specific abundance estimate (with standard error) by the life stage specific survival estimate to first mainstem dam (with Smolts standard error). The standard error around the smolt equivalent estimate is calculated using the following formula; where X = life stage specific juvenile abundance estimate and Y = life stage specific juvenile survival estimate: Var( XY) 22 E()()()()()() X Var Y E Y Var X Var X Var Y This will not be in the raw or summarized performance database. Abundance Run Prediction

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The number of adult returns from a given brood year returning to a point (stream mouth, weir) divided by the number of smolts that left this point 1-5 years prior. Calculated for wild and hatchery origin conventional and captive brood fish separately. Adult data applied in two ways: 1) SAR estimate to stream using population estimate to stream, 2) adult PIT tag SAR estimate to escapement monitoring site (weirs, LGR), and 3) SAR estimate with harvest. Accounts for all harvest below stream.

Smolt-to-adult return rates are generated for four performance periods; tributary to tributary, tributary to tributary, tributary to first mainstem dam, first mainstem dam to first mainstem dam, and first mainstem dam to tributary.

First mainstem dam to first mainstem dam SAR estimates are calculated by dividing the number of PIT tagged adults returning to first mainstem dam by the estimated number of PIT tagged juveniles at first mainstem dam. Variances around the point estimates are calculated as described above.

Tributary to tributary SAR estimates for natural and hatchery origin fish are calculated using PIT tag technology as well as direct counts of fish returning to the drainage. PIT tag SAR estimates are calculated by dividing the number of PIT tag adults returning to the tributary (by life stage and origin type) by the number of PIT tagged juvenile fish migrating from the tributary (by life stage and origin type). Overall PIT tag SAR estimates for natural fish are then calculated by averaging the individual life stage specific SAR’s. Direct counts are calculated by dividing the estimated number of natural and hatchery-origin adults returning to the tributary (by length break-out for natural fish) by the estimated number of Smolt-to-Adult Return Rate natural-origin fish and the known number of hatchery-origin fish leaving the tributary.

Tributary to first mainstem dam SAR estimates are calculated by dividing the number of PIT tagged adults returning to first mainstem dam by the number of PIT tagged juveniles tagged in the tributary. There is no associated variance around this estimate. The adult detection probabilities at first mainstem dam are near 100 percent.

First mainstem dam to tributary SAR estimates are calculated by dividing the number of PIT tagged adults returning to the tributary by the estimated number of PIT tagged juveniles at first mainstem dam. The estimated number of PIT tagged juveniles at first mainstem dam is calculated by multiplying lifestage specific survival estimates (with standard errors) by the number of juveniles PIT tagged in the tributary. The variance for the estimated number of PIT tagged juveniles at first mainstem dam is calculated as follows, where X = the number of PIT tagged fish in the tributary and Y = the variance of the lifestage specific survival estimate: 2 Var( XY) X Var() Y The variance around the SAR estimate is calculated as follows, where X = the number of adult PIT tagged fish returning to the tributary and Y = the estimated number of juvenile PIT tagged fish at first mainstem dam : X EX2 Var() Y Var Y EY() EY 2

Adult to adult calculated for naturally spawning fish and hatchery fish separately as the Progeny-per- Parent Ratio brood year ratio of return adult to parent spawner abundance using data above weir. Two variants calculated: 1) escapement, and 2) spawners. Juvenile production to some life stage divided by adult spawner abundance. Derive adult escapement above juvenile trap multiplied by the pre-spawning mortality estimate. Adjusted for redds above juv. Trap. Recruit per spawner estimates, or juvenile abundance (can be various life stages or Recruit/spawner locations) per redd/female, is used to index population productivity, since it represents the (R/S)(Smolt Equivalents quantity of juvenile fish resulting from an average redd (total smolts divided by total redds) per Redd or female) or female. Several forms of juvenile life stages are applicable. We utilize two measures: 1) juvenile abundance (parr, presmolt, smolt, total abundance) at the tributary mouth, and 2) smolt abundance at first mainstem dam. Percent of female adults that die after reaching the spawning grounds but before spawning. Pre-spawn Mortality Calculated as the proportion of “25% spawned” females among the total number of female carcasses sampled. (“25% spawned” = a female that contains 75% of her egg compliment].

Life stage survival (parr, presmolt, smolt, subyearling) calculated by CJS Estimate Productivity

(SURPH) produced by PITPRO 4.8+ (recapture file included), CI estimated as 1.96*SE. – Juvenile Survival to first Apply survival by life stage to first mainstem dam to estimate of abundance by life stage at mainstem dam the tributary and the sum of those is total smolt abundance surviving to first mainstem dam . Juvenile survival to first mainstem dam = total estimated smolts surviving to first Survival mainstem dam divided by the total estimated juveniles leaving tributary.

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Juvenile survival to first mainstem dam and subsequent Mainstem Dam(s), which is Juvenile Survival to all estimated using PIT tag technology. Survival by life stage to and through the hydrosystem Mainstem Dams is possible if enough PIT tags are available from the stream. Using tags from all life stages combined we will calculate (SURPH) the survival to all mainstem dams. Post-release survival of natural and hatchery-origin fish are calculated as described above Post-release Survival in the performance measure “Survival to first mainstem dam and Mainstem Dams”. No additional points of detection (i.e. screwtraps) are used to calculate survival estimates. Extensive area tributary spawner distribution. Target GPS red locations or reach specific Adult Spawner Spatial summaries, with information from carcass recoveries to identify hatchery-origin vs. Distribution natural-origin spawners across spawning areas within populations. Estimate of the number and percent of hatchery origin fish on the spawning grounds, as the percent within MPG, and percent out of ESU. Calculated from 1) total known origin Stray Rate (percentage) carcasses, and 2) uses fish released above weir. Data adjusted for unmarked carcasses above and below weir. Chinook rearing distribution observations are recorded using multiple divers who follow

Juvenile Rearing protocol described in Thurow (1994). Distribution

Natural fish mortalities are provided to certified fish health lab for routine disease testing Disease Frequency protocols. Hatcheries routinely samples fish for disease and will defer to then for sampling Distribution numbers and periodicity Indices of genetic diversity – measured within a tributary) heterozygosity – allozymes, Genetic Diversity microsatellites), or among tributaries across population aggregates (e.g., FST). Reproductive Success Derived measure: determining hatchery:wild proportions, effective population size is (Nb/N) modeled. Derived measure: the relative production of offspring by a particular genotype. Parentage Relative Reproductive analyses using multilocus genotypes are used to assess reproductive success, mating Success (Parentage) patterns, kinship, and fitness in natural pop8ulations and are gaining widespread use of with

the development of highly polymorphic molecular markers. Derived measure: the number of breeding individuals in an idealized population that would Effective Population Size show the same amount of dispersion of allele frequencies under random genetic drift or the

Genetic (Ne) same amount of inbreeding as the population under consideration. Proportion of escapement composed of adult individuals of different brood years. Calculated for wild and hatchery origin conventional and captive brood adult returns. Accessed via scale method, dorsal fin ray ageing, or mark recoveries. Juvenile Age is determined by brood year (year when eggs are placed in the gravel) Then Age is determined by life stage of that year. Methods to age Chinook captured in screwtrap are by dates; fry – prior to July 1; parr – July 1-August 31; presmolt – September 1 – Age Structure December 31; smolt – January 1 – June 30; yearlings – July 1 – with no migration until following spring. The age class structure of juveniles is determined using length frequency breakouts for natural-origin fish. Scales have been collected from natural-origin juveniles, however, analysis of the scales have never been completed. The age of hatchery-origin fish is determined through a VIE marking program which identifies fish by brood year. For steelhead we attempt to use length frequency but typically age of juvenile steelhead is not calculated. Age distribution of spawners on spawning ground. Calculated for wild and hatchery Age–at–Return conventional and captive brood adult returns. Accessed via scale method, dorsal fin ray ageing, or mark recoveries. Juvenile Age is determined by brood year (year when eggs are placed in the gravel) Then Age is determined by life stage of that year. Methods to age Chinook captured in screwtrap are by dates; fry – prior to July 1; parr – July 1-August 31; presmolt – September 1 – December 31; smolt – January 1 – June 30; yearlings – July 1 – with no migration until following spring. The age class structure of juveniles is determined using length frequency Age–at-Emigration breakouts for natural-origin fish. Scales have been collected from natural-origin juveniles, however, analysis of the scales have never been completed. The age of hatchery-origin fish is determined through a VIE marking program which identifies fish by brood year. For steelhead we attempt to use length frequency but typically age of juvenile steelhead is not calculated. Size distribution of spawners using fork length and mid-eye hypural length. Raw database Size-at-Return measure only. Fork length (mm) and weight (g) are representatively collected weekly from natural juveniles captured in emigration traps. Mean fork length and variance for all samples within a lifestage-specific emigration period are generated (mean length by week then Size-at-Emigration averaged by lifestage). For entire juvenile abundance leaving a weighted mean (by lifestage) is calculated. Size-at-emigration for hatchery production is generated from pre release sampling of juveniles at the hatchery.

Condition factor by life stage of juveniles is generated using the formula: K = (w/l3)(104) Condition of Juveniles at where K is the condition factor, w is the weight in grams (g), and l is the length in Emigration millimeters (Everhart and Youngs 1992). Life History Life

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The percentage of females in the spawning population. Calculated using 1) weir data, 2) Percent Females (adults) total known origin carcass recoveries, and 3) weir data and unmarked carcasses above and below weir. Calculated for wild, hatchery, and total fish. Arrival timing of adults at adult monitoring sites (weir, DIDSON, video) calculated as Adult Run-timing range, 10%, median, 90% percentiles. Calculated for wild and hatchery origin fish separately, and total. This will be a raw database measure only. Spawn-timing

Juvenile emigration timing is characterized by individual life stages at the rotary screw trap Juvenile Emigration and Lower Granite Dam. Emigration timing at the rotary screw trap is expressed as the Timing percent of total abundance over time while the median, 0%, 10, 50%, 90% and 100% detection dates are calculated for fish at first mainstem dam. Unique detections of juvenile PIT-tagged fish at first mainstem dam are used to estimate migration timing for natural and hatchery origin tag groups by lifestage. The actual Median, 0, 10%, 50%, 90% and 100% detection dates are reported for each tag group. Mainstem Arrival Timing Weighted detection dates are also calculated by multiplying unique PIT tag detection by a (Lower Granite) life stage specific correction factor (number fish PIT tagged by lifestage divided by tributary abundance estimate by lifestage). Daily products are added and rounded to the nearest integer to determine weighted median, 0%, 50%, 90% and 100% detection dates. Physical Habitat TBD

Stream Network TBD Passage TBD Barriers/Diversions Instream Flow USGS gauges and also staff gauges Various, mainly Hobo and other temp loggers at screw trap sights and spread out Water Temperature throughout the streams

Chemical Water Quality TBD

Macroinvertebrate TBD Assemblage Fish and Amphibian Observations through rotary screwtrap catch and while conducting snorkel surveys. Habitat Assemblage The number of hatchery juveniles of one cohort released into the receiving stream per year. Hatchery Production Derived from census count minus prerelease mortalities or from sample fish- per-pound Abundance calculations minus mortalities. Method dependent upon marking program (census obtained when 100% are marked). In-hatchery survival is calculated during early life history stages of hatchery-origin juvenile Chinook. Enumeration of individual female's live and dead eggs occurs when the eggs are picked. These numbers create the inventory with subsequent mortality subtracted. This inventory can be changed to the physical count of fish obtained during CWT or VIE In-hatchery Life Stage tagging. These physical fish counts are the most accurate inventory method available. The Survival inventory is checked throughout the year using ‘fish-per-pound’ counts. Estimated survival of various in-hatchery juvenile stages (green egg to eyed egg, eyed egg to ponded fry, fry to parr, parr to smolt and overall green egg to release) Derived from census count minus prerelease mortalities or from sample fish- per-pound calculations minus mortalities. Life stage at release varies (smolt, presmolt, parr, etc.). Mean fork length measured in millimeters and mean weight measured in grams of a Size-at-Release hatchery release group. Measured during prerelease sampling. Sample size determined by individual facility and M&E staff. Life stage at release varies (smolt, presmolt, parr, etc.). Condition Factor (K) relating length to weight expressed as a ratio. Condition factor by life stage of juveniles is generated using the formula: K = (w/l3)(104) where K is the condition Juvenile Condition Factor factor, w is the weight in grams (g), and l is the length in millimeters (Everhart and Youngs 1992). The reproductive potential of an individual female. Estimated as the number of eggs in the Fecundity by Age ovaries of the individual female. Measured as the number of eggs per female calculated by weight or enumerated by egg counter. Spawn date of broodstock spawners by age, sex and origin, Also reported as cumulative Spawn Timing timing and median dates.

Hatchery Broodstock Percent of hatchery broodstock actually used to spawn the next generation of hatchery F1s. Fraction Does not include prespawn mortality. Hatchery Broodstock Percent of adults that die while retained in the hatchery, but before spawning. Prespawn Mortality Female Spawner ELISA Screening procedure for diagnosis and detection of BKD in adult female ovarian fluids. Values The enzyme linked immunosorbent assay (ELISA) detects antigen of R. salmoninarum. Screening procedure for bacterial, viral and other diseases common to juvenile salmonids.

HatcheryMeasures In-Hatchery Juvenile - Gill/skin/ kidney /spleen/skin/blood culture smears conducted monthly on 10 mortalities

In Disease Monitoring per stock

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Mean fork length by age measured in millimeters of male and female broodstock spawners. Length of Broodstock Measured at spawning and/or at weir collection. Is used in conjunction with scale reading Spawner for aging. Percentage of a hatchery group that have retained a mark up until release from the hatchery. Prerelease Mark Retention Estimated from a sample of fish visually calculated as either “present” or “absent” Percentage of a hatchery group that have retained a tag up until release from the hatchery - Prerelease Tag Retention estimated from a sample of fish passed as either “present” or “absent”. (“Marks” refer to adipose fin clips or VIE batch marks). Date and time of volitional or forced departure from the hatchery. Normally determined Hatchery Release Timing through PIT tag detections at facility exit (not all programs monitor volitional releases). Hatchery operational measures included: dissolved oxygen (DO) - measured with DO meters, continuously at the hatchery, and manually 3 times daily at acclimation facilities; Chemical Water Quality ammonia (NH 3 ) nitrite ( NO 2 ), -measured weekly only at reuse facilities (Kooskia Fish Hatchery). Hatchery operational measure (Celsius) - measured continuously at the hatchery with Water Temperature thermographs and 3 times daily at acclimation facilities with hand-held devices.

11.1.2 Indicate whether funding, staffing, and other support logistics are available or committed to allow implementation of the monitoring and evaluation program

Section 11.1.1 describes the methods and plans to address the standards and indicators listed in Section 1.10. The table includes a field indicating whether or not the indicator is being monitored.

For cells with a “Y”, the indicator is being monitored with funding provided by the hatchery mitigation program.

For cells with a “C”, the indicator is being monitored, but is tied to a separately funded program (e.g. Idaho Supplementation Studies (ISS), Idaho Natural Production Monitoring Program (INPM), General Parr Monitoring (GPM) program etc.). Without continued funding for these programs, many of the M&E components will not occur. For example, The ISS program is scheduled to end in 2014 with some components ending in 2012. Funding to offset this loss needs to be identified to avoid significant M&E data gaps.

For cells with a “Y/C”, the indicator is being monitored and is partially funded through the hatchery mitigation program. Other programs, such as those listed in 2b above, provide the remaining funding.

For cells with an “N”, the indicator is not currently being monitored. For all applicable indicators that are not being addressed (N), a brief narrative is provided below describing why that particular indicator is not being monitored.

Standard or Indicator - Standards are in bold font, Indictors are in italic font and underlined

3.2 The current status and trends of natural origin populations likely to be impacted by hatchery production are monitored.- With the existing infrastructure, we can monitor abundance and productivity of the natural population in the uppermost reaches of the SF Clearwater River (in Red River and Crooked River). Assessing these parameters in the lower S.F. Clearwater will require new infrastructure.

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3.4 Effects of strays from hatchery programs on non-target (unsupplemented and same species) populations remain within acceptable limits.- Representative fish from all release groups are tagged with CWT and PITs. If fish from these releases are recovered as strays, PITs and CW will identify their cohort and origin. Additionally, since 2008 all broodstock used to generate releases have been tissue sampled as part of a Parental Based Tagging (PBT) program. This will allow any fish released from any of the hatcheries in Idaho to be assigned to their hatchery of origin and to a specific cohort. To date, only tissue samples have been collected. Funding to genotype and maintain that genetic database is still lacking.

3.5 Habitat is not a limiting factor for the affected supplemented population at the targeted level of supplementation.- While specific habitat capacity is not monitored, managers do not feel that the number of juveniles released for supplementation will exceed habitat carrying capacity.

3.6 Supplementation of natural population with hatchery origin production does not negatively impact the viability of the target population.- Chinook salmon populations in the Clearwater River were extirpated and subsequently reestablished primarily with Rapid River hatchery stock. We do not have the pre-hatchery influenced period data on abundance and productivity in the Clearwater River to compare to a post treatment supplementation management. Adult abundance is monitored at Red River, Crooked River, American River, Lolo Creek and several tributaries in the Lochsa and Selway Rivers. Juvenile production monitoring (screw traps and snorkeling) does occur annually through the ISS and INPM programs.

3.7.2 Natural spawning success of hatchery-origin fish must be similar to that of natural-origin fish.- Genetic samples are collected from all Chinook salmon passed above the weirs on Red, Crooked River, and Lolo Creek (check with NPT), and Crooked Fork Creek. This will allow the ability to assign progeny to the parents released above the weirs. There is currently no funding available to process and analyze these samples. We are unable to monitor reproductive success of fish spawning below the weirs on Red and Crooked rivers

3.10.1 Detectable changes in rate of occurrence and spatial distribution of disease, parasite or pathogen among the affected hatchery and natural populations - IDFG maintains a formalized fish health monitoring program for stocks propagated and reared at the hatchery facilities. IDFG has not prioritized the need to develop a formalized monitoring program for natural populations adjacent to the hatchery program. However, if mortalities occur or are observed during routine field operations and data collection events, samples are collected and delivered to the IDFG Fish Health Lab for analysis. Additionally, fish health samples collected by the USFWS as part of the National Wild Fish Heath Survey Database (www.esg.montana.edu/nfhdb/) are collected throughout Idaho.

For hatchery-origin releases, between 45 and 30 d prior to release, a 60 fish pre-liberation sample is taken from each rearing lot to assess the prevalence of viral replicating agents and to detect the pathogens responsible for bacterial kidney disease and whirling disease. In addition, an organosomatic index is developed for each release lot. Diagnostic services are provided by the IDFG Fish Health Laboratory.

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4.4.3 Samples of natural populations for disease occurrence before and after artificial production releases See 3.10.1 above

11.2) Indicate risk aversion measures that will be applied to minimize the likelihood for adverse genetic and ecological effects to listed fish resulting from monitoring and evaluation activities.

Risk aversion measures for monitoring and evaluation activities associated with the evaluation of the Lower Snake River Compensation Program are specified in our ESA Section 7 Consultation and Section 10 Permit 1124. A brief summary of the kinds of actions taken is provided.

Adult handling activities are conducted to minimize impacts to ESA-listed, non-target species. Adult and juvenile weirs and screw traps are engineered properly and installed in locations that minimize adverse impacts to both target and non-target species. All trapping facilities are constantly monitored to minimize a variety of risks (e.g., high water periods, high emigration or escapement periods, security).

Adult spawner and redd surveys are conducted to minimize potential risks to all life stages of ESA-listed species. The IDFG conducts formal redd count training annually. During surveys, care is taken to not disturb ESA-listed species and to not walk in the vicinity of completed redds.

Snorkel surveys conducted primarily to assess juvenile abundance and density are conducted in index sections only to minimize disturbance to ESA-listed species. Displacement of fish is kept to a minimum.

Marking and tagging activities are designed to protect ESA-listed species and allow mitigation harvest objectives to be pursued/met. Hatchery produced fish are visibly marked to differentiate them from their wild/natural counterpart.

SECTION 12. RESEARCH

12.1 OBJECTIVE OR PURPOSE

Indicate why the research is needed, its benefit or effect on listed natural fish populations, and broad significance of the proposed project

Hatchery Supplementation Research The Idaho Salmon Supplementation (ISS) research study was initiated to evaluate the benefits and risks of using a supplementation strategy to increase natural production. It is the only large scale study of its kind in the Columbia Basin. The ISS project has utilized existing hatchery facilities that are funded by the LSRCP program and used LSRCP Page 79

program fish to create supplementation broodstocks. For obvious reasons, the LSRCP and ISS programs are tightly linked with respect to monitoring and evaluating both hatchery- and natural-origin Chinook salmon associated with and adjacent to the hatchery program. This research program is scheduled to be completed in 2014.

The following excerpts were taken from the 1997-2001 ISS progress report (Lutch et al. 2003):

The Idaho Supplementation Studies (ISS) project is a collaborative study between Idaho Department of Fish and Game (IDFG), the Nez Perce Tribe, the Shoshone Bannock Tribe, and the U.S. Fish and Wildlife Service. It was developed to determine the benefits and risks associated with hatchery supplementation of Chinook salmon Oncorhynchus tshawytscha in the Snake River basin. Because the scope of study is broad, streams included were distributed among the cooperating agencies, which operate under an umbrella agreement to maintain consistency for all research activities.

The ISS study design was implemented in 1992 (Bowles and Leitzinger 1991) with the following goals in mind: 1) evaluate the efficacy of using hatchery fish to restore or augment production in natural populations of spring and summer Chinook salmon in the Salmon and Clearwater River subbasins of Idaho, 2) evaluate the long-term impacts of supplementation with hatchery origin Chinook salmon on the survival and fitness of natural populations, and 3) evaluate hatchery releases at different life stages with respect to these same measures of production and productivity. To achieve these goals, a long-term experiment was designed to compare production and productivity measures between a group of experimentally supplemented (treatment) streams and a group of untreated (control) streams where natural production has experienced little or no hatchery influence. The following objectives were established to accomplish the goals of the ISS study:

1. Monitor and evaluate the effects of supplementation on the abundance of naturally produced juveniles and resultant adult returns,

2. Monitor and evaluate changes in natural productivity and genetic composition of target and adjacent populations following supplementation,

3. Determine which supplementation strategies (e.g., smolt versus parr release) provide the highest response in natural production without adverse affects on productivity, and

4. Develop supplementation recommendations.

Research tasks are distributed among three project phases. During Phase I, broodstock for the first generation (F1) of supplementation treatments was developed from crosses of locally derived hatchery and wild/natural origin Chinook salmon. These F1 fish were incubated in the hatchery and reared to parr, presmolt, or smolt life stages. They were uniquely marked prior to release in natural rearing areas to make them distinguishable from other hatchery origin and

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naturally produced Chinook salmon. During Phase II of the study, adult returns from F1 supplementation releases were crossed with adult returns from naturally produced juveniles. Natural origin adults comprise a minimum of 50% of the fish used in the crosses to produce the second generation (F2) of supplementation fish. All remaining natural origin and supplementation recruits are allowed to spawn naturally, as long as supplementation adults do not numerically exceed the number of natural fish. In Phase III, supplementation with juvenile outplants ceases, but adult returns from supplementation juveniles are allowed to enter natural spawning areas and spawn with each other or fish of natural origin to naturally supplement the F3 generation. Monitoring and evaluation of juvenile production and resulting adult returns are conducted on the F1, F2, and F3 generations to provide a means to evaluate the effects of supplementation on natural production and productivity.

Continuous coordination between the LSRCP hatchery evaluation study, Idaho Department of Fish and Game’s BPA-funded ISS research is required because these programs overlap in several areas including: juvenile outplanting, broodstock collection, spawning (mating) strategies, and natural production and productivity monitoring.

12.2 COOPERATING AND FUNDING AGENCIES

U.S. Fish and Wildlife Service – Lower Snake River Compensation Plan Office

Supplementation research is funded by Bonneville Power Administration

12.3 PRINCIPLE INVESTIGATOR OR PROJECT SUPERVISOR AND STAFF

Dan Schill – Fisheries Research Manager, Idaho Department of Fish and Game. Dave Venditti- Sr. Fisheries Research Biologist, IDFG- ISS evaluation

12.4 STATUS OF STOCK, PARTICULARLY THE GROUP AFFECTED BY PROJECT, IF DIFFERENT THAN THE STOCK(S) DESCRIBED IN SECTION 2

N/A

12.5 TECHNIQUES: INCLUDE CAPTURE METHODS, DRUGS, SAMPLES COLLECTED, TAGS APPLIED

Idaho supplementation studies staff work cooperatively to assemble annual juvenile Chinook salmon out-migration and adult return data sets. Weir traps and screw traps are used to capture emigrating juvenile Chinook salmon. Generally, all target species captured are anesthetized and handled. A portion of captured juveniles may be fin-clipped or PIT-tagged. Adult information is assembled from a variety of information sources including: dam and weir counts, fishery

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information, coded-wire tag information, redd surveys, and spawning surveys.

Idaho Department of Fish and Game and cooperator staff may sample adults to collect tissue samples for subsequent genetic analysis. Additionally, otoliths, scales, or fins may be collected for age analysis.

12.6 DATES OR TIME PERIOD IN WHICH RESEARCH ACTIVITY OCCURS

Fish culture practices are monitored throughout the year by hatchery and hatchery evaluation research staff.

Adult escapement monitoring occurs May through September.

Juvenile trapping and tagging occurs February through November. Smolt out-migration through the hydro system corridor is typically monitored from March through September. Juvenile population abundance and density are monitored during late spring and summer months.

Fish health monitoring occurs year round.

12.7 CARE AND MAINTENANCE OF LIVE FISH OR EGGS, HOLDING DURATION, TRANSPORT METHODS

Research activities that involve the handling of eggs or fish apply the same protocols reviewed in Section 9 above. Hatchery staff generally assists with all cooperative activities involving the handling of eggs or fish.

12.8 EXPECTED TYPE AND EFFECTS OF TAKE AND POTENTIAL FOR INJURY OR MORTALITY

See Appendix A; Table 1b. Generally, take for research activities is defined as: “observe/harass”, “capture/handle/release” and “capture, handle, mark, tissue sample, release.”

12.9 LEVEL OF TAKE OF LISTED FISH: NUMBER OR RANGE OF FISH HANDLED, INJURED, OR KILLED BY SEX, AGE, OR SIZE, IF NOT ALREADY INDICATED IN SECTION 2 AND THE ATTACHED “TAKE TABLE

12.10 ALTERNATIVE METHODS TO ACHIEVE PROJECT OBJECTIVES

Alternative methods to achieve research objectives have not been developed.

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12.11 LIST SPECIES SIMILAR OR RELATED TO THE THREATENED SPECIES; PROVIDE NUMBER AND CAUSES OF MORTALITY RELATED TO THIS RESEARCH PROJECT

N/A

12.12 INDICATE RISK AVERSION MEASURES THAT WILL BE APPLIED TO MINIMIZE THE LIKELIHOOD FOR ADVERSE ECOLOGICAL EFFECTS, INJURY, OR MORTALITY TO LISTED FISH AS A RESULT OF THE PROPOSED RESEARCH ACTIVITIES

See Section 11.2 above.

SECTION 13. ATTACHMENTS AND CITATIONS

LITERATURE CITED

Berkson, J. 1991. Lyons Ferry fall Chinook wire tag analysis. Portland, OR. Columbia River Inter-Tribal Fish Commission.

Bowles, E. C. and E. Leitzinger. 1991. Salmon supplementation studies in Idaho rivers: experimental design. Idaho Department of Fish and Game, prepared for U.S. Department of Energy, Bonneville Power Administration, Contract DE-BI79-89BP01466, Project 89- 098. 167 pp.

Chapman, D., A. Giorgi, M. Hill, A. Maule, S. McCutcheon, D. Park, W. Platts, K. Prat, J. Seeb, L. Seeb and others. 1991. Status of Snake River Chinook Salmon. Pacific Northwest Utilities Conference Committee, 531 p. D. Chapman Consultants, Boise, ID.

Cramer, S. P. 1995. Selway genetic resource assessment, supplement to Nez Perce Tribal Hatchery genetic risk assessment. S.P. Cramer & Associates, Inc. Contract report to Nez Perce Tribal Executive Committee, Lapwai, ID.

Cramer, S.P. and F. Neeley. 1992. Genetic risk assessment of the Nez Perce Tribal Hatchery master plan. Prepared for Nez Perce Tribal Department of Fisheries Resources Management. Lapwai, ID.

Galbreath, P.F., C.A. Beasley, B.A. Berejikian, R.W. Carmichael, D.E. Fast, M. J. Ford, J.A. Hesse, L.L. McDonald, A.R. Murdoch, C.M. Peven, and D.A. Venditti. 2008. Recommendations for Broad Scale Monitoring to Evaluate the Effects of Hatchery Supplementation on the Fitness of Natural Salmon and Steelhead Populations; Final Report of the Ad Hoc Supplementation Monitoring and Evaluation Workgroup.

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http://www.nwcouncil.org/fw/program/2008amend/uploadedfiles/95/Final%20Draft%20 AHSWG%20report.pdf

Hesse, J.A., P.J. Cleary, and B.D. Arnsberg. 1995. Salmon supplementation studies in Idaho Rivers. Annual Report. Prepared for Bonneville Power Administration. Project No. 89- 098-2.

Hoss, S.A. 1970. Reintroductions of salmon and steelhead into portions of the Clearwater River drainage. Annual project Report, July 1, 1968 to June 30, 1969. Columbia River Fishery Development Program. Project No. 161.22A. Contract No. 14-17-0001-1860. Idaho Department of Fish and Game, Boise, ID.

Idaho Department of Fish and Game. 1992. Anadromous Fish Management Plan 1992-1996. Idaho Department of Fish and Game, Boise, Idaho.

Idaho Department of Fish and Game. 2001. IDFG Fisheries Management Plan 2001-2006. Idaho Department of Fish and Game, Boise, Idaho.

Kiefer, S., M. Rowe and K. Hatch. 1992. Stock Summary Reports for Columbia River Anadromous Salmonids Volume V: Idaho Final Draft for The Coordinated Information System. Idaho Department of Fish and Game

Larson, R.E. and L. Mobrand. 1992. Nez Perce Tribal Hatchery Master Plan and Appendices. Nez Perce Tribe. Mobrand Biometrics. Bonneville Power Administration, Division of Fish and Wildlife. Portland, OR.

Mathews, G.M. and R.S. Waples. 1991. Status review of Snake River spring and summer Chinook salmon. U.S. Department of Commerce, NOAA Technical Memorandum, NMFS F/FWC-200. Seattle, WA.

Murphy, L.W. and H.E. Metsker. 1962. Inventory of Idaho streams containing anadromous fish including recommendations for improving production of salmon and steelhead. Part II: Clearwater River drainage. Idaho Department of Fish and Game and U.S. Fish and Wildlife Service.

Nez Perce Tribe and Idaho Department of Fish and Game. 1990. Clearwater River Subbasin Salmon and Steelhead Production Plan. Funded by the Northwest Power Planning Council; Columbia Basin Fish and Wildlife Authority.

Northwest Power and Conservation Council (NPCC). 2001. Draft Salmon Subbasin Summary. Prepared for the Northwest Power and Conservation Council, Portland, OR.

Northwest Power and Conservation Council (NPCC). 2006. Draft Guidance for Developing Monitoring and Evaluation as a Program Element of the Fish and Wildlife Program. (NPCC Document 2006-4). Portland, Oregon. (http://www.nwcouncil.org/library/2006/draftme.htm).

Piper, G. R., I. B. McElwain, L. E. Orme, J. P. McCraren, L. G. Gowler, and J. R. Leonard.

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1982. Fish Hatchery Management. U.S. Fish and Wildlife Service, Washington, D.C.

Shoen, D., R.M. Jones, and P.K. Murphy. 1999. Section 7 Watershed Biological Assessment Lochsa River drainage Clearwater subbasin: determination of effects of ongoing activities based on the matrix of pathways and indicators of watershed condition for steelhead trout, fall Chinook salmon and bull trout. U.S. Department of Agriculture, U.S. Forest Service, Clearwater National Forest.

U.S. Fish and Wildlife Service. 1999. Draft lower Snake River juvenile salmon migration feasibility study. Prepared for the U.S. Army Corps of Engineers, Walla Walla District.

Walters, J., J. Hansen, J. Lockhart, C. Reighn, R. Keith, and J. Olson. 2001. Idaho supplementation studies. Five-year report 1992 – 1996. Idaho Department of Fish and Game. Project Report No. 99-14, Contract DE-BI19-89BP01466. Prepared for the Bonneville Power Administration. Portland, OR.

Waples, R.S., R.P. Jones, B.R. Beckman, and G.A. Swan. 1991. Status review for Snake River fall Chinook salmon. U.S. Department of Commerce. NOAA Technical Memorandum NMFS F/NWC-201.

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SECTION 14. CERTIFICATION LANGUAGE AND SIGNATURE OF RESPONSIBLE PARTY

“I hereby certify that the information provided is complete, true and correct to the best of my knowledge and belief. I understand that the information provided in this HGMP is submitted for the purpose of receiving limits from take prohibitions specified under the Endangered Species Act of 1973 (16 U.S.C.1531-1543) and regulations promulgated thereafter for the proposed hatchery program, and that any false statement may subject me to the criminal penalties of 18 U.S.C. 1001, or penalties provided under the Endangered Species Act of 1973.”

Name, Title, and Signature of Applicant:

Certified by______Date:______

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SECTION 15. PROGRAM EFFECTS ON OTHER (NON-ANADROMOUS SALMONID) ESA-LISTED POPULATIONS

15.1 LIST ALL ESA PERMITS OR AUTHORIZATIONS FOR ALL NON- ANADROMOUS SALMONID PROGRAMS ASSOCIATED WITH THE HATCHERY PROGRAM ESA Section 6 Cooperative Agreement for Bull Trout Take Associated with IDFG Research

IDFG annually prepares a bull trout conservation program plan and take report, which describes their management program for bull trout to meet the provisions contained in Section 6 of the ESA and to comport with the spirit of Section 10(a)1(A). This plan identifies the benefits to bull trout resulting from management and research conducted or authorized by the state, provides documentation of bull trout take conducted and authorized by IDFG and provides an estimate of take for the coming year. Each year the report is submitted to the USFWS, which then makes a determination whether this program is in accordance with the ESA. The plan/report is due to USFWS by March 31 annually. A summary of recent take in the Clearwater subbasin is further discussed in Section 15.3 of this HGMP.

ESA Section 7 Consultation and Biological Opinions

ESA Section 7 Consultation and Biological Opinion through the U.S. Fish and Wildlife Service Lower Snake Compensation Program for bull trout take associated with hatchery operations.

15.2 DESCRIPTION OF NON-ANADROMOUS AQUATIC SPECIES AND HABITAT THAT MAY BE AFFECTED BY HATCHERY PROGRAM

This program releases juvenile hatchery spring Chinook into the Clearwater River subbasin and bull trout (threatened) are the only non-anadromous aquatic ESA-listed species in the subbasin. Bull trout life history, status and habitat use in Clearwater River subbasin is summarized below.

General Species Description, Status, and Habitat Requirements

Bull trout (members of the family Salmonidae) are a species of char native to Nevada, Oregon, Idaho, Washington, Montana and western Canada. While bull trout occur widely across the western United States, they are patchily distributed at multiple spatial scales from river basin to local watershed, and individual stream reach levels. Due to widespread declines in abundance, bull trout were initially listed as threatened in Idaho in 1998, and listed throughout their coterminous range in the United States in 1999. On January 13, 2010, the USFWS proposed to revise its 2005 designation of critical habitat for bull trout, which includes a substantial portion of the Clearwater River subbasin (1,679 stream miles were proposed as critical habitat in the Clearwater River subbasin).

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Throughout their range, bull trout have declined due to habitat degradation and fragmentation, blockage of migratory corridors, poor water quality, past fisheries management (such as over harvest and bounties), and the introduction of non-native species such as brown, lake and brook trout. Range-wide, several local extinctions have been documented. Many of the remaining populations are small and isolated from each other, making them more susceptible to local extinctions. However, recent work in Idaho concluded that despite declines from historical levels, Idaho bull trout are presently widely distributed, relatively abundant, and apparently stable (High et al. 2008). High et al. (2008) further concluded that the Clearwater River bull trout Recovery Unit exhibited an overall increasing trend, with three of four available post-1994 abundance trends significantly positive in this subbasin, although the subbasin had the lowest mean linear bull trout density of all recovery units sampled across Idaho (1.2 bull trout/100 m in the Clearwater River recovery unit compared to the high of 22.1 bull trout/100 m in the Clark Fork River recovery unit).

Bull trout exhibit a wide variety of life history types, primarily based on general seasonal migration patterns of subadult and adult bull trout between headwater spawning and rearing streams to other habitats (usually downstream) for foraging and overwintering, including resident (residing in small headwater streams for their entire lives); fluvial (migrating to larger river systems); adfluvial (migrating to lakes or reservoirs); and anadromous (migrating to estuarine or marine waters) (Goetz et al. 2004). All of these life history strategies are present in the Clearwater River subbasin, except anadromy. Fluvial and resident bull trout populations have been commonly observed throughout the current range of bull trout in the Clearwater River subbasin (USFWS 2002). There are two naturally adfluvial bull trout populations within the Clearwater River Recovery Unit. One is associated with Fish Lake in the upper North Fork Clearwater River drainage and the other is associated with Fish Lake in the Lochsa River drainage (USFWS 2002), both of which are outside the influence of this spring Chinook hatchery program.

Bull trout spawning and rearing requires cold water temperatures; generally below 16°C during summer rearing, and less than about 10°C during spawning (Dunham et al. 2003). Juvenile bull trout require complex rearing habitats (Dambacher and Jones 1997, Al-Chokhachy et al. 2010). Migratory adult and subadult bull trout are highly piscivorous (Lowery et al. 2009). Additionally, migratory adults need unobstructed connectivity to diverse habitats where forage fish species are plentiful and where water temperatures are relatively cool (less than about 18°C maximum during migration) (Howell et al. 2009).

Population Status and Distribution by Core Area

Bull trout are distributed throughout most of the large rivers and associated tributary systems of the Clearwater River subbasin. The Clearwater River Recovery Unit consists of 7 core areas, with a total of 45 local populations distributed among them as defined in the bull trout Draft Recovery Plan (USFWS 2002). The recovery team also identified 27 potential local populations. The Clearwater spring Chinook program releases hatchery juveniles into four bull trout core areas, including the South Fork Clearwater, Lower and Middle Fork Clearwater, Lochsa, and Selway rivers. The following information on these four bull trout core areas and local population status and habitat use within them, is summarized from the bull trout Draft Recovery Plan (USFWS 2002) unless otherwise cited.

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South Fork Clearwater River Core Area The South Fork Clearwater River Core Area has the most comprehensive data for bull trout within the Clearwater River Recovery Unit obtained through a multi-year study by IDFG that documented juvenile distribution in most tributaries and headwater streams. Bull trout are currently known to use spawning and rearing habitat in five stream complexes within the South Fork Clearwater, which are defined as local populations in the Draft Recovery Plan. These local populations include Red River (including Upper and West Fork of South Fork Red River), Crooked River, Newsome Creek, Tenmile Creek, and Johns Creek. Potential local populations include American River, Meadow Creek, and Mill Creek. The current abundance and distribution of bull trout in the core area is considered lower than historic levels, with low incidence of fluvial migratory adults, indicating the predominance of a resident life history. Significant fluvial bull trout migration occurs in the Crooked River watershed.

The bull trout 5-year status review conducted in 2006 (USFWS 2008) determined the South Fork Clearwater River Core Area had adult abundance levels in the 1,000-2,500 fish range, occupation of stream miles in the 125-650-mile range, an unknown short-term trend, substantial/imminent threat to persistence, and a final ranking of “at risk” to become extirpated (Table 26). More recent analysis by High et al. (2008) determined that a negative rate of population change occurred pre-1994, but post-1994 was significantly positive overall, indicating an increasing population trend post-1994 (19-year record at 85 survey sites) (see Table 26).

Table 26. Summary table of core area rankings for population abundance, distribution, trend, threat, and final rank, Clearwater River Recovery Unit (USFWS 2008).

Source: USFWS (2008) Table 27. Intrinsic rates of population change (r) with 90% confidence limits (CLs) for bull trout in the core areas of the Clearwater River Recovery Unit of Idaho with available data.

Source: High et al. (2008) Note: The sampling method used in each drainage or area is shown (S = snorkeling, R = redd count). Trends in r were evaluated for the period before 1994, the period after 1994, and all years; asterisks indicate trends that were significant (i.e., confidence intervals did not include zero). Estimates that were unavailable due to inadequate data are indicated (NA). Page 89

Lochsa River Core Area Bull trout are currently known to use spawning and rearing habitat in 16 streams or stream complexes within the Lochsa River drainage. These local populations include Fishing (Squaw), Legendary Bear (Papoose), Boulder, Fox, Shotgun, Crooked Fork/Hopeful, Rock, Haskell, Colt Killed (White Sands), Beaver, Storm, Brushy Fork, Spruce, Twin, Walton, and Lower Warm Springs creeks. Potential local populations include Post Office, Weir, Indian Grave, Lake, Fish, Hungary, Boulder, Old Man, Split, Fire, Coolwater, Canyon, Deadman, and Pete King creeks. Fluvial bull trout are thought to use the majority of spawning and rearing habitat except for Spruce and Shotgun creeks, which are likely resident populations due to migration barriers. Subadult and adult bull trout are suspected to use nearly all accessible areas of the core area for foraging and migration.

The bull trout 5-year status review conducted in 2006 (USFWS 2008) determined the Lochsa River Core Area had adult abundance levels in the 50-250 range, occupation of stream miles in the 125-650 range, a stable short-term trend, moderate/imminent threat to persistence, and a final ranking of “at risk” to become extirpated (Table 26). More recent analysis by High et al. (2008) determined that a negative rate of population change occurred pre-1994, but post-1994 was significantly positive overall, indicating an increasing population trend post-1994 (19-year record at 43 survey sites) (Table 27). Furthermore, the rate of increase in the Lochsa River Core Area post-1994 was the highest of 4 core areas analyzed in the Clearwater River Recovery Unit, and the second highest of 17 core areas analyzed in Idaho.

Selway River Core Area The Selway River supports significant fluvial bull trout populations that are widely distributed through the core area in variable densities, as well as widely distributed resident local populations in some upper tributary reaches. Local populations are well-connected within this core area. Bull trout are currently known to use spawning and rearing habitat in at least 10 streams or stream complexes within the Selway River drainage. These local populations include Meadow, Moose, Running, White Cap, Bear, Deep, Indian, and Magruder creaks, and the Upper Selway and Little Clearwater rivers. Potential local populations include Marten, Mink, Gedney, Three Links, and O’Hara creeks. Intensive distribution surveys have not been conducted throughout the core area, and additional undocumented spawning and rearing areas likely exist. Total abundance is unknown, but stream survey data collected in 1997 suggest that fish density is relatively high.

The bull trout 5-year status review conducted in 2006 (USFWS 2008) determined the Selway River Core Area had an unknown adult abundance level, occupation of stream miles in the 125- 650 range, an unknown short-term trend, widespread/low-severity threat to persistence, and a final ranking of “potential risk” to become extirpated (Table 26). More recent analysis by High et al. (2008) determined that a significantly positive rate of population change occurred pre- 1994, and post-1994 was stable overall, indicated by the near zero rate of change (19 years of record at 26 sites).

Lower and Middle Fork Clearwater River Core Area Adult and subadult bull trout probably use the lower (mainstem) Clearwater River, Middle Fork Clearwater River, and their tributaries primarily as foraging, migratory, subadult rearing, and overwintering habitat, although the extent of use is unclear. Bull trout abundance is at very low

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levels within this core area. No tributary streams have current documentation of bull trout spawning; however, Lolo Creek has documented occurrence of juvenile bull trout. Lolo Creek is considered a local population because some small juveniles have been found above a small falls that would preclude fish of their size from migrating upstream to this location. Clear Creek is the only potential local population. In Clear Creek, 2 to 4 bull trout are collected annually at a salmon trap during spring and released above the trap. Length of captured bull trout has been 254 to 356 mm.

The bull trout 5-year status review conducted in 2006 (USFWS 2008) determined the Lower and Middle Fork Clearwater River Core Area had an unknown adult abundance level, occupation of stream miles in the 125-650-mile range, an unknown short-term trend, substantial/imminent threat to persistence, and a final ranking of “at risk” to become extirpated (Table 26). This core area was not evaluated by High et al. (2008).

15.3 ANALYSIS OF EFFECTS

Direct Effects

Direct effects primarily arise through collection of spring Chinook broodstock. Migratory bull trout are captured in the Crooked River trap, Walton Creek trap, and Clear Creek trap targeting spring Chinook salmon. A variable number of upstream migrant bull trout are captured, bio- sampled, and passed upstream of these traps each year. Traps may also have a short-term effect through potential alternation of migration routes or delay in movement.

A small percentage of bull trout sampled in a fish trap may be injured or killed (generally less than 1%) as evidenced by the very small level of mortality reported by IDFG (IDFG 2006, 2007, 2008, 2009). Adult trapping activities have occurred for many years in the Clearwater River subbasin and have not apparently hindered positive population growth rates of bull trout since 1994, as evidenced by results of High et al. (2008), and are not expected to limit bull trout population growth rates into the future.

Competition is possible between subadult bull trout and hatchery spring Chinook juveniles if some residualize. Because these species evolved sympatrically in the Clearwater River subbasin, some form of resource partitioning would be expected. In addition, Chinook salmon residualism is suspected to be an uncommon life history strategy. Therefore, potential competition is not expected to be a primary limiting factor for bull trout. On the contrary, release of juvenile hatchery Chinook likely provides increased forage (beneficial effect) for migratory adult and subadult bull trout, which are highly piscivorous.

Indirect Effects

Indirect effects may arise through hatchery operations such as water withdrawals, effluent discharge, routine operations and maintenance activities, non-routine operations and maintenance activities (e.g., intake excavation, construction, emergency operations, etc.). Hatchery operations are not expected to affect bull trout population productivity. These activities have occurred for many years in the Clearwater River subbasin and apparently haven’t hindered positive population growth rates of bull trout since 1994, as evidenced by results of High et al. (2008), and are not expected to limit bull trout population growth rates into the future.

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Cumulative Effects

Cumulatively, the effects of the Clearwater spring Chinook hatchery program and associated monitoring and evaluation results in increased forage for migratory adult and subadult bull trout and contributes knowledge on bull trout population distribution and abundance through incidental captures in broodstock collection traps. Such knowledge can be used to evaluate bull trout population trends over time, such as the analysis conducted by High et al. 2008.

Take

Annual bull trout take in the form of observation, capture, handling, and bio-sampling occurs each year at various broodstock collection traps and through associated monitoring and evaluation studies. At the end of each year bull trout take is quantified and projected for the upcoming year’s operations and monitoring in a report prepared by IDFG (the Idaho Bull Trout Conservation Plan and Take Report). Take is derived from observing or capture and handling of bull trout through a variety of survey methods, including snorkeling, redd surveys, electrofishing, hook-and-line, weir trapping, screw trapping, and seining. Between 2005 and 2009 inclusive, a total of 134, 68, and 3 bull trout were captured at Crooked River, Powell, and Red River adult trap respectively. During the same time period, no incidental mortality of bull trout associated with trapping operations occurred.

15.4 ACTIONS TAKEN TO MITIGATE FOR POTENTIAL EFFECTS

Actions taken by IDFG to minimize adverse effects on bull trout include:

1. Continue fish health practices to minimize the incidence of infectious disease agents. Follow IHOT, AFS, and PNFHPC guidelines.

2. Monitor hatchery effluent to ensure compliance with National Pollutant Discharge Elimination System permit.

3. Continue Hatchery Evaluation Studies (HES) to provide comprehensive monitoring and evaluation for LSRCP Chinook, which provide valuable incidental bull trout data.

4. Conduct adult trapping activities to minimize impacts to bull trout and other non-target species. Trapping provides valuable incidental bull trout data.

5. Prepare annual bull trout conservation program plan and take report, submitted to USFWS, to ensure compliance with the ESA.

15.5 REFERENCES

Al-Chokhachy, R., B. Roper, T. Bowerman, P. Budy. 2010. Review of bull trout habitat associations and exploratory analyses of patterns across the interior Columbia River Basin. North American Journal of Fisheries Management 30:464-480.

Dambacher, J.M., and K.K. Jones. 1997. Stream habitat of juvenile bull trout populations in Oregon, and benchmarks for habitat quality. Pages 350-360 in W.C. Mackay, M.K. Brewin and M. Monita, editors. Friends of the Bull Trout Conference Proceedings. Trout Unlimited Canada, Calgary, Alberta.

Dunham, J., Rieman, B. & Chandler, G. 2003. Influences of temperature and environmental variables on the distribution of bull trout within streams at the southern margin of its range. North American Journal of Page 92

Fisheries Management 23:894–904.

Goetz, F.A., E. Jeanes, and E. Beamer. June 2004. Bull trout in the nearshore, preliminary draft. U.S. Army Corps of Engineers, Seattle District.

High, B., K.A. Meyer, D.J. Schill, and E.R.J. Mamer. 2008. Distribution, abundance, and population trends of bull trout in Idaho. North American Journal of Fisheries Management 28:1687–1701.

Howell, P.J., J.B. Dunham, and P.M. Sankovich. 2009. Relationships between water temperatures and upstream migration, cold water refuge use, and spawning of adult bull trout from the Lostine River, Oregon, USA. Ecology of Freshwater Fish: DOI 10.1111/j.1600 0633.2009.00393.x.

IDFG (Idaho Department of Fish and Game). 2006. 2006 bull trout conservation program plan and 2005 report. Dated April 2006, Report No. 06-11.

IDFG (Idaho Department of Fish and Game). 2007. 2007 bull trout conservation program plan and 2006 report. Dated May 2007.

IDFG (Idaho Department of Fish and Game). 2008. 2008 bull trout conservation program plan and 2007 bull trout take report. Dated May 2008.

IDFG (Idaho Department of Fish and Game). 2009. 2009 bull trout conservation program plan and 2008 bull trout take report. Dated April 2009.

Lowery, E.D. 2009. Trophic relations and seasonal effects of predation on Pacific salmon by fluvial bull trout in a riverine food web. M.S. thesis, University of Washington, Seattle, WA.

USFWS (U.S. Fish and Wildlife Service). 2002. Chapter 16, Clearwater River Recovery Unit, Idaho. 196 p. In: U.S. Fish and Wildlife Service. Bull Trout (Salvelinus confluentus) Draft Recovery Plan. Portland, Oregon.

USFWS. 2008. Bull Trout (Salvelinus confluentus) 5-Year Review: Summary and Evaluation. Portland, OR. http://www.fws.gov/pacific/bulltrout/5-yr%20Review/BTFINAL_42508.pdf.

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Appendix A

Table 1a. Estimated take of ESA listed species resulting from hatchery programmatic maintenance activities at Clearwater Fish Hatchery satellite facilities. Listed species affected: summer steelhead DPS/Population: Snake River/Lochsa River Activity: Hatchery Programmatic Maintenance (See section 2.2.3 for description of activities) Location of activity: Powell Satellite Facility Annual Take of Listed Fish By Life Stage (Number of Fish) Maintenance Activity Type of Take Egg/Fry Juvenile/Smolt Adult Carcass Observe or harass a) Hatchery Diversion and Capture, handle, and release c) 10 water source Unintentional lethal take g) 1 intake Other Take (specify) h) Observe or harass a) Capture, handle, and release c) 10 Adult fish weir Unintentional lethal take g) 1 Other Take (specify) h) Observe or harass a) River bank Capture, handle, and release c) 10 stabilization Unintentional lethal take g) 1 Other Take (specify) h) Observe or harass a) 0 Capture, handle, and release c) 30 TOTAL Unintentional lethal take g) 3 Other Take (specify) h) 0 Listed species affected: summer Steelhead DPS/Population: Snake River/ S.F. Clearwater River Activity: Hatchery Programmatic Maintenance Location of activity: Red River Satellite Facility Annual Take of Listed Fish By Life Stage (Number of Fish)

Maintenance Activity Type of Take Egg/Fry Juvenile/Smolt Adult Carcass Observe or harass a) Hatchery Diversion and Capture, handle, and release c) 10 water source Unintentional lethal take g) 1 intake Other Take (specify) h) Observe or harass a) Capture, handle, and release c) 10 Adult fish weir Unintentional lethal take g) 1 Other Take (specify) h)

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Observe or harass a) River bank Capture, handle, and release c) 10 stabilization Unintentional lethal take g) 1 Other Take (specify) h) Observe or harass a) 0 Capture, handle, and release c) 30 TOTAL Unintentional lethal take g) 3 Other Take (specify) h) 0 Listed species affected: summer Steelhead DPS/Population: Snake River/ S.F. Clearwater River Activity: Hatchery Programmatic Maintenance Location of activity: Crooked River Satellite Facility Annual Take of Listed Fish By Life Stage (Number of Fish)

Maintenance Egg/Fr Juvenile/Smo Activity Type of Take y lt Adult Carcass Observe or harass a) Hatchery Diversion and Capture, handle, and release c) 10 water source Unintentional lethal take g) 1 intake Other Take (specify) h) Observe or harass a) Capture, handle, and release c) 10 Adult fish weir Unintentional lethal take g) 1 Other Take (specify) h) Observe or harass a) River bank Capture, handle, and release c) 10 stabilization Unintentional lethal take g) 1 Other Take (specify) h) Observe or harass a) 0 Capture, handle, and release c) 30 TOTAL Unintentional lethal take g) 3 Other Take (specify) h) 0

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Table 1b. Estimated take of ESA listed species resulting from research/monitoring activities. Take for juvenile trapping is covered under an annually renewed 4d Research permit for the Idaho Chinook Supplementation Study (2010- 14706) Listed species affected: Summer Steelhead ESU/Population: Snake River DPS/S.F. Clearwater R. Population Activity: Juvenile Screw Traps Location of research activity: Red ,Crooked, American rivers Dates of activity: March-November (annually) Research program operator: Dave Venditti (IDFG) Annual Take of Listed Fish By Life Stage (Number of Fish) Type of Take Egg/Fry Juvenile/Smolt Adult Carcass Observe or harass a) Collect for transport b) Capture, handle, and release c) 15,000 Capture, handle, tag/mark/tissue sample, release d) 1,500 Removal (e.g. broodstock) e) Intentional lethal take f) Unintentional lethal take g) 160 Other Take (specify) h) Tissue sampling Listed species affected: Summer Steelhead DPS/Population: Snake River DPS/Lochsa R. Population. Activity: Juvenile Screw Traps Location of research activity: Crooked Fork Creek, Colt Killed Creek; Dates of activity: March-November Research program operator: Dave Venditti (IDFG) Annual Take of Listed Fish By Life Stage (Number of Fish) Type of Take Egg/Fry Juvenile/Smolt Adult Carcass Observe or harass a) Collect for transport b) Capture, handle, and release c) 900 Capture, handle, tag/mark/tissue sample, release d) 4,400 Removal (e.g. broodstock) e) Intentional lethal take f) Unintentional lethal take g) 53 Other Take (specify) h) Tissue sampling

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Appendix B.

Responses to the issues and recommendations made by the USFWS Hatchery Review Team (HRT) specific to the Clearwater Fish Hatchery spring Chinook Salmon program.

Category HRT # Issue / Recommendation Managers Response to Comment

Establish program goals; quantify harvest, conservation, and CW21a Addressed in HGMP. escapement goals for all releases (smolts and adult outplants)

Modify planning and mgmt CW21b documents so all goals are stated Addressed in HGMP. consistently

Spring Chinook populations that spawn naturally in the Clearwater basin all

originate from supplementation programs or opportunistic straying from hatchery production within the Basin. The RM&E program under development to address the hydrosystem biological Develop a long term master plan for opinion will provide information that re-introducing SPCHK into will facilitate development of suitable CW22a Clearwater. Long term conservation escapement goals for these natural and genetic management plan, populations. Criteria for developing alongside harvest. these goals will be consistent with goals

Program Goals and Objectives and Goals Program used for ESA listed populations in the Salmon River. In the interim populations within the Clearwater Basin will be managed consistent with the IDFG and Tribal resource management plans. Managers will establish long term abundance, productivity, spatial Long term goals should include the structure and diversity goals based on CW22b most likely natural population criteria consistent with those used for structure for viability ESA listed populations in the Salmon River Basin.

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Managers have initiated expansion of

rearing capacity at Clearwater Hatchery to offset realized versus modeled smolt to adult survivals. Managers are also experimenting with a small release of Re-evaluate LSRCP mitigation goals summer run Chinook salmon in portions CW23 for this stock, in light of current of the basin to evaluate the possibility mainstem conditions that they are better suited to local habitat and environmental conditions and will achieve SARs closer to those originally modeled. Modifications of the

Program Goals and Objectives and Goals Program program to accommodate these changes will require new funding. Managers do prioritize use of locally adapted hatchery fish for broodstock but have also prioritized meeting broodstock goals over the perceived Discontinue backfilling Clearwater risks of utilizing non-locally adapted fish production with Rapid River fish; so from the parent stock at Rapid River. CW24a as to facilitate the further When backfilling is necessary managers development of locally adapted attempt to back fill from sites from broodstock within the Clearwater Basin but will use

the original parent stock from Rapid

River Hatchery if no in-basin alternative

ction is available.

Discontinue exchanging eggs CW24b between the two locally adapted see CW24a broodstocks

If backfilling continues, mark these fish differently so as not to include them in future broodstocks. CW24c see CW24a Discourage backfilling where natural

Broodstock Choice andColle Choice Broodstock populations are trying to be re- established. Develop a SPCHK reintroduction plan for the Selway, using a local CW25a see CW22a broodstock, emphasize stock viability

Discontinue exchanging eggs and CW25b fish between broodstocks and/or see CW24a watersheds

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If backfilling continues, mark these fish differently so as not to include them in future broodstocks. CW25c see CW24a

Discourage backfilling where natural

Collection Choice and and Choice Broodstock Broodstock populations are trying to be re- established. Managers have historically implemented adult outplants to utilize abundant returns to hatcheries to supplement natural spawning in the Clearwater Basin that originated from the same Discontinue adult outplanting across CW26a parent stock (Rapid River Hatchery) as river systems. the current hatchery population. Adult outplants to supplement natural populations will likely continue until natural populations have recovered to self sustaining levels.

Discontinue transfer of adults see CW26a - all hatchery fish outplanted CW26b collected at Rapid River (out of are carefully screened for disease issues

basin, fish health risk) prior to any outplanting.

Pre-smolt release are stipulated in the current US vs. OR agreement and constitute and extremely small fraction Discontinue trapping adults for of the overall hatchery production. They broodstock needed for pre-smolt are only released into areas that cannot CW27a releases; allow these adults to be accessed for smolt releases in the spawn naturally. spring. Currently there is only one release (300,000) of sub-yearling Chinook salmon from Clearwater Fish

Hatchery. Hatchery and Natural Spawning Natural and Hatchery Any presmolt releases must be CW27b included in a master plan and spell see CW22a & b and CW27a out the goals of these releases.

Spawning on site is not feasible because Spawn adults at Red River; bringing of elevated water temperatures. Adults CW28a adults to the hatchery increases fish transported to Clearwater Hatchery are health risks isolated from on-site juvenile production. Each female is sampled for BKD, and 60 Sample each female, at spawning, fish are sampled for virus. Whirling for virus; cull eggs if necessary. disease is also sampled using standard CW28b Incubate all eggs separately until pathology protocol. All egg families are fish health results are in incubated separately and culled as needed.

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Anesthetic is not used on adults. There

Find alternative to MS-222 for is no fish anesthetic labeled for CW29 adults; allows other (beneficial) use immediate release, there is a three day of carcasses withdrawal anesthetic.

This recommendation has been Discontinue erythromycin injections CW30 incorporated into standard hatchery of adult CHK passed upstream. practices.

Fish are examined for gross lesions, and Hold all carcasses from outplanting CW31 clean looking carcasses are utilized for

Hatchery and Natural Spawning Natural and Hatchery until fish health checks are done nutrients.

IDFG has scaled back on use of

prophylactic feeding and is evaluating Re-evaluate the need for regular the feasibility of discontinuing the use of CW32 prophylactic use of erythromycin in erythromycin feed in most cases. We

Rearing feed are no longer using erythromycin in the

Incubation and and Incubation feed at Clearwater hatchery.

Sample 60 fish for pre-release Sample size of 60 fish is now standard at CW33 inspections. IDFG facilities.

Assess oxygen content in water Smolts are held off feed for minimum of during crowding and loading to 48 before transport and transport tanks CW34 determine if low enough to impact are pre-charged with oxygen and chilled

post release survival or cold water. Periodically tank D.O.'s Release and Outmigration Releaseand are monitored. This recommendation is being considered by the hatchery staff to Construct shade covers over CW10 determine if it is a practical solution and

raceways. able to be implemented with existing hatchery practices. Ensure water diverted for fish This water is measured monthly and production is measured and use is reported through the NPDES permit. CW11 reported to USFWS Region 1, This is available to other agencies as Engineering, Division of Water needed. Resources. This recommendation is being Construct shade covers for adult Facilities and Operations Facilitiesand considered by the hatchery staff to holding ponds at Red River Satellite CW35 determine if it is a practical solution and for relief of warm water to make able to be implemented with existing adult holding better hatchery practices.

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Complete or replace the water intake weir at Red River Satellite to LSRCP is in process of developing the CW36 maintain water to the facility and solution to this recommendation.

protect resident fish in the area.

Find alternative methods to install, LSRCP is in process of developing the CW36 clean, and maintain adult picket solution to this recommendation. weir at Red River Satellite

Redesign the Powell fish trap to improve human safety (?) and to LSRCP is in process of developing the CW37 reduce broodstock injury. Also solution to this recommendation.

improve broodstock sorting. Facilities and Operations Facilitiesand Delay transfer of juvenile fish to Juvenile fish are not transferred to the Powell Acclimation Pond until water pond until likelihood of freezing event is CW38 source is not susceptible to freezing. low. Onsite staff monitors the pond Develop written emergency intake continuously until all fish have management plan for facility been released. Managers have continued to expand tagging and sampling rates for coded- wire tags in fisheries to improve harvest contribution estimates. Managers believe that Genetics Parental Based Tagging (PBT) will allow all fish to be Work with co managers to assess uniquely marked for subsequent sub-

the mark sampling program with the lethal sampling at all life states. Because CW16 goal of increasing the percent of PBT effectively marks all fish released CWT's recovered in terminal from a hatchery the mark rate issue fisheries. goes away and precision of stock contributions estimates in mixed stock fisheries should improve markedly with no increase in sampling rates. Funding is required to investigate the utility of Parental Based Tagging; that technology may replace CWTs. Coded-wire tagging goals and objectives Work with Co managers to develop are described in the annual AOP a data management plan that document for this facility. Reporting of incorporates tagging goals and CW17 tagged juvenile releases and tag Research Monitoring and Accountability and Monitoring Research objectives, data management, and recoveries among returning adults are reporting requirements of CWT data submitted to RMIS within the specified at both program and regional levels. reporting periods. Hatchery production reports are Continue to work through the current, M&E reports have been CW18 backlog of reports. Complete reformatted and IDFG is working with annual reports in a timely fashion. the LSRCP office to bring all reporting requirements up to date.

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Tribal, state and federal co-managers meet via teleconference weekly to report and discuss in season run strength estimates, harvest allocations, Work with co manager to develop a and hatchery returns. Co-managers CW19 mechanism to address and report in discuss in-season harvest management, season contingencies. broodstock management and distribution of fish in excess of brood needs. Co-managers also conduct a pre- season planning meeting and a post season de-briefing meeting. Funding is required to investigate the Ensure tagging strategy accurately utility of Parental Based Tagging; that CW39 represents entire population for a technology may replace CWTs. The issue particular brood year of CWT representation has been addressed. Spring Chinook populations that spawn naturally in the Clearwater basin all originated from supplementation programs or opportunistic straying from hatchery production within the Basin. The RM&E program under development Once a conservation and to address the hydrosystem biological reintroduction plan for Clearwater opinion will provide information that CW40 SPCHK is in place, make sure it has will facilitate development of suitable

Research Monitoring and Accountability and Monitoring Research an adequate M&E plan to monitor escapement goals for these natural its progress populations. Criteria for developing these goals will be consistent with goals used for ESA listed populations in the Salmon River. In the interim populations within the Clearwater Basin will be managed consistent with the IDFG and Tribal resource management plans. Properly clean and disinfect all Managers implement best management equipment used in the basin that is practices that are consistent with CW41 transferred among different river existing federal/state guidelines for systems, to prevent transfer of screening and disinfection of disease or ANS. equipment.

Issue is currently being addressed through an annual statement of work negotiated between IDFG and LSRCP and coordinated through Annual dOutreach Update information available to CW20 Operating Plan process. Requires public. maintenance of funding for M&E tasks. Managers also make in-season information about hatchery returns and

Education an Education harvests on publicly accessible websites.

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